shuvadipkhanra
commented
2 months ago make -j 16
| _make lib make[1]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0' make -C src make[2]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src' make -C lib make[3]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib' make dirslinks make[4]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib' Updating links to used modules in all directories make ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links ../xdrfile.links make[5]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib' make -C ../analysis links make -C ../asmjit links make -C ../bias links make -C ../blas links make -C ../cltools links make -C ../colvar links make -C ../config links make -C ../core links make -C ../function links make -C ../generic links make -C ../gridtools links make -C ../isdb links make -C ../lapack links make -C ../lepton links make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/blas' make -C ../main links make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config' make -C ../mapping links Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/blas Nothing to do in /home/shuvadip/Downloads/plumed-2.9.0/src/config make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config' make -C ../molfile links make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/blas' make -C ../multicolvar links make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lapack' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/cltools' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/bias' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/function' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/analysis' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/lapack Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/cltools make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lepton' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/bias Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/function Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/analysis make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/isdb' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/main' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/molfile' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/lepton make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/mapping' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/main Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/isdb Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/molfile make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/generic' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/asmjit' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/gridtools' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/mapping make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/colvar' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/core' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/asmjit make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/molfile' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/gridtools Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/generic make -C ../reference links Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/colvar Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/core make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/asmjit' make -C ../secondarystructure links make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/multicolvar' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/secondarystructure' make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lapack' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/multicolvar make -C ../setup links make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/main' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/secondarystructure make -C ../tools links make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/reference' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/reference make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/setup' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/setup make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lepton' make -C ../vatom links make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/vatom' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/vatom make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/tools' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/tools make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/bias' make -C ../vesselbase links make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/colvar' make -C ../wrapper links make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/core' make -C ../xdrfile links make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/generic' make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/gridtools' make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/reference' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/wrapper' make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/setup' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/xdrfile' Nothing to do in /home/shuvadip/Downloads/plumed-2.9.0/src/wrapper make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/wrapper' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/xdrfile make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/xdrfile' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/vesselbase' Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/vesselbase make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/vatom' make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/secondarystructure' make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/cltools' make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/mapping' make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/tools' make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/function' make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/multicolvar' make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/isdb' make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/analysis' make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/vesselbase' make[5]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib' make[4]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib' make dirs make[4]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib' Compiling all directories make ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper ../xdrfile make[5]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib' make -C ../analysis obj make -C ../asmjit obj make -C ../bias obj make -C ../blas obj make -C ../cltools obj make -C ../colvar obj make -C ../config obj make -C ../core obj make -C ../function obj make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/blas' make -C ../generic obj make -C ../gridtools obj compiling blas.cpp make -C ../isdb obj make -C ../lapack obj make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config' make PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt make -C ../lepton obj make -C ../main obj make -C ../mapping obj make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/bias' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/analysis' compiling AnalysisBase.cpp make[7]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/cltools' Updating ConfigInstall.inc make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/main' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/function' compiling ABMD.cpp make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lapack' compiling CLTool.cpp make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lepton' compiling main.cpp compiling Combine.cpp make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/asmjit' compiling CompiledExpression.cpp make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/isdb' compiling lapack.cpp make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/gridtools' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/generic' compiling arch.cpp make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/mapping' compiling Caliber.cpp make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/colvar' make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/core' compiling ActionWithGrid.cpp compiling AdaptivePath.cpp compiling Angle.cpp compiling Debug.cpp compiling ActionAnyorder.cpp cmp -s ConfigInstall.inc~ ConfigInstall.inc | cp ConfigInstall.inc~ ConfigInstall.inc rm ConfigInstall.inc~ Updating Config.inc make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/blas' compiling Cell.cpp cmp -s Config.inc~ Config.inc | cp Config.inc~ Config.inc rm Config.inc~ Updating version.h make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lapack' { ../maketools/make-scripts-options.sh ; cat completion.sh ; } | ../maketools/xxd > completion.xxd Updating config.txt file compiling ExpressionProgram.cpp compiling assembler.cpp make[7]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config' make Config.o ConfigInstall.o compile_options.sh make[7]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config' cat ../../Makefile.conf | ../maketools/xxd > Makefile.conf.xxd main.cpp: In function ‘int main(int, char**)’: main.cpp:39:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 39 | for(unsigned iarg=1; iarg<argc; iarg++) { | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
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| In file included from xdrfile/../../xdrfile/xdrfile_trr.h:64, from xdrfile/xdrfile_trr.h:1, from Driver.cpp:41: xdrfile/../../xdrfile/xdrfile.h:32:2: warning: "/*" within comment [-Wcomment] 32 | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
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| In file included from xdrfile/xdrfile_xtc.h:1, from Driver.cpp:42: xdrfile/../../xdrfile/xdrfile_xtc.h:32:2: warning: "/*" within comment [-Wcomment] 32 | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
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| compiling ActionWithInputGrid.cpp AdaptivePath.cpp: In constructor ‘PLMD::mapping::AdaptivePath::AdaptivePath(const PLMD::ActionOptions&)’: AdaptivePath.cpp:154:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 154 | for(int i=0; i<getNumberOfReferencePoints(); ++i) { | ~^ |
if(tindex+1<var[iarg].size()) end=tindex+2; | if(ipoint==tindex) x0=0; | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
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| In file included from xdrfile/../../xdrfile/xdrfile_xtc.h:64, from xdrfile/xdrfile_xtc.h:1, from DumpAtoms.cpp:34: xdrfile/../../xdrfile/xdrfile.h:32:2: warning: "/*" within comment [-Wcomment] 32 | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
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| In file included from xdrfile/xdrfile_trr.h:1, from DumpAtoms.cpp:35: xdrfile/../../xdrfile/xdrfile_trr.h:32:2: warning: "/*" within comment [-Wcomment] 32 | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
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| ActionAtomistic.cpp: In member function ‘void PLMD::ActionAtomistic::requestAtoms(const std::vector |
if(indexes[i].index()>=n) { std::string num; Tools::convert( indexes[i].serial(),num ); error("atom " + num + " out of range"); } | for(int i=0; i<natoms; i++) for(int k=0; k<3; k++) { | ~^ |
for(int j=0; j<nval; j++) { | ~^~~~~ ActionAtomistic.cpp:122:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 122 | for(int j=0; j<natoms; j++) positions[j]=pbc.realToScaled(positions[j]); | ~^ |
for(int j=0; j<natoms; j++) positions[j]=pbc.scaledToReal(positions[j]); | ~^ |
for(int j=0; j<natoms; j++) positions[j]=savedPositions[j]; | ~^ |
for(int j=0; j<nval; j++) valueboxj=a->getOutputQuantity(j); | ~^~~~~ ActionAtomistic.cpp:135:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 135 | for(int j=0; j<nval; j++) { | ~^~~~~ ActionAtomistic.cpp:139:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 139 | for(int i=0; i<natoms; i++) for(int k=0; k<3; k++) { | ~^ |
for(unsigned i=0; i<n; i++) t.push_back(AtomNumber::index(i)); | ~^~ ActionAtomistic.cpp:185:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 185 | for(unsigned i=0; i<n; i++) t.push_back(AtomNumber::index(i)); | ~^~
compiling Average.cpp
ExpressionTreeNode.cpp: In constructor ‘PLMD::lepton::ExpressionTreeNode::ExpressionTreeNode(PLMD::lepton::Operation*, const std::vector |
if (operation->getNumArguments() != children.size()) | if (operation->getNumArguments() != children.size()) | if (operation->getNumArguments() != children.size()) | if (operation->getNumArguments() != children.size()) | if (numTags == examples.size()) { | for (int i = 0; i < examples.size(); i++) { | for (int j = 0; matches && j < getChildren().size(); j++) | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
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| In file included from xdrfile/../../xdrfile/xdrfile_trr.h:64, from xdrfile/xdrfile_trr.h:1, from Driver.cpp:41, from DriverDouble.cpp:23: xdrfile/../../xdrfile/xdrfile.h:32:2: warning: "/*" within comment [-Wcomment] 32 | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
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| In file included from xdrfile/xdrfile_xtc.h:1, from Driver.cpp:42, from DriverDouble.cpp:23: xdrfile/../../xdrfile/xdrfile_xtc.h:32:2: warning: "/*" within comment [-Wcomment] 32 | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
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| compiling ParsedExpression.cpp compiling constpool.cpp compiling ActionRegister.cpp compiling cpuinfo.cpp compiling ActionWithIntegral.cpp compiling CS2Backbone.cpp compiling func.cpp compiling BiasValue.cpp compiling Constant.cpp ParsedExpression.cpp: In static member function ‘static PLMD::lepton::ExpressionTreeNode PLMD::lepton::ParsedExpression::substituteSimplerExpression(const PLMD::lepton::ExpressionTreeNode&, std::map<int, PLMD::lepton::ExpressionTreeNode>&)’: ParsedExpression.cpp:225:17: warning: ‘first’ may be used uninitialized in this function [-Wmaybe-uninitialized] 225 | if (first == 0.0) // Subtract from 0 | ^~ In file included from ParsedExpression.cpp:67: Operation.h:1003:33: warning: ‘second’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1003 | AddConstant(double value) : value(value) { | ^ |
double first, second; // if yes, value of first and second child | ^ |
if (pos != tokens.size()) | if (pos != tokens.size()) | if (pos == tokens.size()) | if (pos == tokens.size() | tokens[pos].getType() != ParseToken::RightParen) | if (pos == tokens.size() | tokens[pos].getType() != ParseToken::RightParen) | for (int i = 0; i < node.getChildren().size(); i++) { | for (int i = 1; i < args.size(); i++) | for (int i = 0; i < variablesToCopy.size(); i++) | for (int step = 0; step < operation.size(); step++) { | for (int i = 0; i < args.size(); i++) | if (rc != iov[i].iov_len) | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { | if (input_integer[0] != dcdcordmagic) { | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; | if ((tmpbuf[2Li]+tmpbuf[2Li+1L]) != sizeof(float)*N) return DCD_BADFORMAT; | static void swap2_aligned(void *v, ptrdiff_t ndata) { | ^ |
static void swap2_unaligned(void *v, ptrdiff_t ndata) { | ^ |
static int fio_write_str(fio_fd fd, const char *str) { | ^ |
static int fio_read_int32(fio_fd fd, int *i) { | ^ |
static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { | ^ |
for(unsigned i=istart; i<iend+1; ++i) sfrac[i] = target*(i-istart); | ~^ |
for(unsigned i=istart; i<iend; ++i) sfrac[i] = dr*(i-istart); | ~^~~~~ PathReparameterization.cpp:102:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 102 | if( cfin==iend && k>= iend+1 ) plumed_merror("path reparameterization error"); | else if( cfin==(iend+1) && k>=iend ) { k=iend-1; break; } | else if( cfin==(iend-1) && k<=iend ) { k=iend+1; break; } | if( ifix2<(mypath.size()-1) ) reparameterizePart( ifix2, mypath.size()-1, target, TOL ); | for(int i=0; i<npar; i++) { | ~^~~~~ ActionWithArguments.cpp:286:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 286 | for(int j=0; j<nval; j++) { | ~^~~~~ ActionWithArguments.cpp:292:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 292 | for(int j=0; j<nval; j++) { | ~^~~~~ ActionWithArguments.cpp:294:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 294 | if( v->hasDerivatives() ) for(int i=0; i<npar; i++) v->addDerivative(i,(value[i*nval+j]-a->getOutputQuantity(j))/std::sqrt(epsilon)); | ~^~~~~ compiling EuclideanDissimilarityMatrix.cpp compiling ConvertToFES.cpp compiling gromacsplugin.cpp compiling FarthestPointSampling.cpp In file included from gromacsplugin.cpp:62: Gromacs.h: In function ‘int PLMD::molfile::mdio_readline(PLMD::molfile::md_file, char, int, int)’: Gromacs.h:467:14: warning: ignoring return value of ‘char fgets(char, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 467 | fgets(buf, n, mf->f); | static void swap2_aligned(void *v, ptrdiff_t ndata) { | ^ |
static void swap8_unaligned(void *v, ptrdiff_t ndata) { | ^ |
static void swap4_unaligned(void *v, ptrdiff_t ndata) { | ^ |
static void swap2_unaligned(void *v, ptrdiff_t ndata) { | ^ |
return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
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| In file included from xdrfile/../../xdrfile/xdrfile_trr.h:64, from xdrfile/xdrfile_trr.h:1, from Driver.cpp:41, from DriverFloat.cpp:23: xdrfile/../../xdrfile/xdrfile.h:32:2: warning: "/*" within comment [-Wcomment] 32 | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
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| In file included from xdrfile/xdrfile_xtc.h:1, from Driver.cpp:42, from DriverFloat.cpp:23: xdrfile/../../xdrfile/xdrfile_xtc.h:32:2: warning: "/*" within comment [-Wcomment] 32 | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
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| compiling globals.cpp compiling inst.cpp compiling PathTools.cpp compiling EndPlumed.cpp compiling pdbplugin.cpp compiling logging.cpp compiling operand.cpp In file included from pdbplugin.cpp:64: periodic_table.h:173:12: warning: ‘int PLMD::molfile::get_pte_idx(const char*)’ defined but not used [-Wunused-function] 173 | static int get_pte_idx(const char *label) | ^ |
return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | return builtin___strncpy_chk (dest, src, len, | __glibc_objsize (__dest)); | for(int i=0; i<nbefore; ++i) { | ~^ |
static bool vMemMgrCheckTree(VMemMgr* self) noexcept { | ^ |
if(largest*2<natoms) unique_serial=true; | for(int i=0; i<count; i++) { | ~^ |
if( gatindex.size()==natoms ) { | if( gatindex[i]!=i ) { shuffledAtoms=1; break; }
Atoms.cpp: In member function ‘void PLMD::Atoms::setAtomsContiguous(int)’:
Atoms.cpp:464:21: warning: comparison of integer expressions of different signedness: ‘std::vector |
if(gatindex.size()<natoms) shuffledAtoms=1; | for(unsigned i=0; i<natoms; i++) fullList[i]=i; | ~^ |
for(int i=0; i<vecs.size(); i++) { | ~^ |
for(unsigned int i=0; i<isz1; i++) | ~^~~~~ Dimer.cpp:220:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 220 | for(unsigned int i=0; i<isz2; i++) | ~^~~~~
Dimer.cpp: In member function ‘void PLMD::colvar::Dimer::consistencyCheck()’:
Dimer.cpp:309:20: warning: comparison of integer expressions of different signedness: ‘std::vector |
if(dsigmas.size()!=nranks && dsigmas.size()!=1) | for(int i=0; i<ovmd_.size(); ++i) { | ~^ |
for(unsigned i=0; i<nexp; ++i) { | ~^~~~~
compiling Group.cpp
EMMI.cpp: In member function ‘void PLMD::isdb::EMMI::get_GMM_d(std::string)’:
EMMI.cpp:1121:22: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator |
if(GMM_dbeta[i]>=GMM_dgrps.size()) error("Check Beta values"); MetaD.cpp: In constructor ‘PLMD::bias::MetaD::MetaD(const PLMD::ActionOptions&)’: MetaD.cpp:1238:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1238 | if(result!=0&&result!=mpinw) error("in this WALKERS_MPI run some replica have restarted from GRID while other do not!"); | if(result!=0&&result!=mpinw) error("in this WALKERS_MPI run some replica have restarted from FILE while other do not!"); | p=std::fabs(p); min1=3.0xmq-std::fabs(tol1q); min2=std::fabs(eq); | ~^~ tools/../../tools/Brent1DRootSearch.h:86:20: note: ‘e’ was declared here 86 | double cx=bx, d, e, min1, min2, fc=fb, p, q, r, s, tol1, xm; | ^
In file included from tools/../../tools/RootFindingBase.h:26,
from tools/RootFindingBase.h:1,
from ContourFindingBase.h:26,
from FindContourSurface.cpp:23:
tools/../../tools/Brent1DRootSearch.h: In member function ‘void PLMD::RootFindingBase |
p=std::fabs(p); min1=3.0xmq-std::fabs(tol1q); min2=std::fabs(eq); | ~^~ tools/../../tools/Brent1DRootSearch.h:86:20: note: ‘e’ was declared here 86 | double cx=bx, d, e, min1, min2, fc=fb, p, q, r, s, tol1, xm; | ^
compiling GridPrintingBase.cpp
compiling GenExample.cpp
compiling GridSearch.cpp
In file included from tools/../../tools/RootFindingBase.h:26,
from tools/RootFindingBase.h:1,
from ContourFindingBase.h:26,
from FindSphericalContour.cpp:23:
tools/../../tools/Brent1DRootSearch.h: In member function ‘void PLMD::RootFindingBase |
p=std::fabs(p); min1=3.0xmq-std::fabs(tol1q); min2=std::fabs(eq); | ~^~ tools/../../tools/Brent1DRootSearch.h:86:20: note: ‘e’ was declared here 86 | double cx=bx, d, e, min1, min2, fc=fb, p, q, r, s, tol1, xm; | ^
compiling Piecewise.cpp
Plumed.cpp: In member function ‘virtual void PLMD::generic::Plumed::prepare()’:
Plumed.cpp:323:26: warning: comparison of integer expressions of different signedness: ‘std::vector |
bool redo=(index.size()!=n); | for(int i=0; i<forces.size(); i++) forces[i]=0.0; | ~^ |
for(int i=0; i<masses.size(); i++) masses[i]=getMass(i); | ~^ |
for(int i=0; i<charges.size(); i++) charges[i]=getCharge(i); | ~^ |
if(ncp>4*comm.Get_size()) { | if(ncp>4*comm.Get_size()) { | if(!pbc[i] && i0>=nbin[i]) found=false; GridVessel.cpp:421:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const value_type’ {aka ‘const unsigned int’} [-Wsign-compare] 421 | if( pbc[i] && i0>=nbin[i]) i0%=nbin[i];
compiling OutputPDBFile.cpp
TrigonometricPathVessel.cpp: In member function ‘virtual void PLMD::mapping::TrigonometricPathVessel::finish(const std::vector |
if( iclose3<0 | iclose3>=mymap->getFullNumberOfTasks() ) { | Value* val = myv->copyOutput( key ); | ^~~ DataFetchingObject.cpp: In static member function ‘static void PLMD::DataFetchingObject::get_shape(const PLMD::ActionSet&, const string&, const string&, const PLMD::TypesafePtr&)’: DataFetchingObject.cpp:99:10: warning: unused variable ‘val’ [-Wunused-variable] 99 | Value* val = myv->copyOutput( key ); | ^~~
compiling x86inst.cpp
compiling Jcoupling.cpp
compiling MetainferenceBase.cpp
compiling ExtraCV.cpp
compiling x86instimpl.cpp
compiling InterpolateGrid.cpp
compiling GenJson.cpp
compiling RandomExchanges.cpp
compiling x86internal.cpp
compiling PrintDissimilarityMatrix.cpp
compiling ExchangePatterns.cpp
make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/mapping'
make -C ../multicolvar obj
make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/multicolvar'
compiling ActionVolume.cpp
compiling FlexibleBin.cpp
compiling GenericMolInfo.cpp
compiling Target.cpp
compiling ReadAnalysisFrames.cpp
compiling Read.cpp
../maketools/makecmd map < GREX.cpp > GREXMap.inc
compiling ResetCell.cpp
compiling Fake.cpp
../maketools/makecmd enum < GREX.cpp > GREXEnum.inc
compiling Time.cpp
compiling GenTemplate.cpp
compiling AlphaBeta.cpp
compiling Info.cpp
compiling kT.cpp
make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/gridtools'
compiling Manual.cpp
compiling MovingRestraint.cpp
compiling PBMetaD.cpp
compiling UpdateIf.cpp
compiling PdbRenumber.cpp
compiling pesmd.cpp
make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/function'
compiling SimpleMD.cpp
compiling SumHills.cpp
compiling Completion.cpp
compiling GHBFIX.cpp
SimpleMD.cpp: In member function ‘void PLMD::cltools::SimpleMD::compute_forces(int, double, double, const std::vector<PLMD::VectorGeneric<3> >&, const double*, double, const std::vector<std::vector |
for(int jlist=0; jlist<list[iatom].size(); jlist++) { | for(int i=0; i<list.size(); i++) list_size+=list[i].size(); | ~^ |
for(int i=0; i<list.size(); i++) list_size+=list[i].size(); | ~^ |
for(auto i=0; i<etas.size(); i++) etas[i]*=units.getEnergy()/atoms.getUnits().getEnergy(); | ~^ |
static bool ZoneHeap_hasDynamicBlock(ZoneHeap self, ZoneHeap::DynamicBlock block) noexcept { | ^ |
p=std::fabs(p); min1=3.0xmq-std::fabs(tol1q); min2=std::fabs(eq); | ~^~ tools/../../tools/Brent1DRootSearch.h:86:20: note: ‘e’ was declared here 86 | double cx=bx, d, e, min1, min2, fc=fb, p, q, r, s, tol1, xm; | ^ compiling FilterBetween.cpp compiling FilterLessThan.cpp compiling ActionWithInputVessel.cpp compiling DLLoader.cpp compiling PlumedMain.cpp make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/asmjit' make -C ../wrapper obj make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/wrapper' compiling PlumedStatic.cpp compiling DynamicList.cpp compiling Plumed.c compiling Selector.cpp compiling ERMSD.cpp compiling MultiDomainRMSD.cpp make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/wrapper' make -C ../xdrfile obj make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/xdrfile' compiling ActionWithVessel.cpp compiling xdrfile.cpp xdrfile.cpp:30:2: warning: "/*" within comment [-Wcomment] 30 | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
|---|
| In file included from xdrfile.cpp:85: xdrfile.h:32:2: warning: "/*" within comment [-Wcomment] 32 | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
|---|
| xdrfile.cpp: In function ‘int PLMD::xdrfile::sizeofint(int)’: xdrfile.cpp:529:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 529 | while (size >= num && num_of_bits < 32) | while (bytes[num_of_bytes] >= num) | if (num_of_bits >= num_of_bytes * 8) | for (i = 0; i < num_of_bytes; i++) | for (i = 0; i < num_of_bytes-1; i++) | if (lastbits < num_of_bits) | if(size3>xfp->buf1size) | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp; | ^ xdrfile.cpp:819:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 819 | int smallidx, minidx, maxidx; | ^ |
int smallnum, smaller, larger, i, is_smaller, run; | ^ |
if(size3>xfp->buf1size) | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) | ^ xdrfile.cpp:1169:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 1169 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp; | ^ xdrfile.cpp:1301:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1301 | if(tmp==(unsigned int)buf2[0]) | int errval=1; | ^ |
if(size3>xfp->buf1size) | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp; | ^ xdrfile.cpp:1315:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 1315 | int smallidx, minidx, maxidx; | ^ |
int smallnum, smaller, larger, i, is_smaller, run; | ^ |
if(size3>xfp->buf1size) { | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { | ^ xdrfile.cpp:1652:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 1652 | maxidx = (LASTIDX<tmp) ? LASTIDX : tmp; | ^ xdrfile.cpp:1762:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1762 | if(tmp==(unsigned int)buf2[0]) | int errval=1; | ^ |
if (size > maxsize) | ^~ xdrfile.cpp:2363:22: note: ‘size’ was declared here 2363 | unsigned int size; | ^~~~ xdrfile.cpp: In function ‘int PLMD::xdrfile::xdrfile_compress_coord_float(float, int, float, PLMD::xdrfile::XDRFILE)’: xdrfile.cpp:1185:42: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1185 | abs(thiscoord[2] - prevcoord[2]) < larger) { | abs(thiscoord[1] - prevcoord[1]) < larger && | abs(thiscoord[0] - prevcoord[0]) < larger && | abs(thiscoord[2] - prevcoord[2]) < larger) { | abs(thiscoord[1] - prevcoord[1]) < larger && | abs(thiscoord[0] - prevcoord[0]) < larger && | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
|---|
| In file included from xdrfile_trr.cpp:66: xdrfile.h:32:2: warning: "/*" within comment [-Wcomment] 32 | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
|---|
| In file included from xdrfile_trr.cpp:67: xdrfile_trr.h:32:2: warning: "/*" within comment [-Wcomment] 32 | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
|---|
| xdrfile_trr.cpp: In function ‘int PLMD::xdrfile::do_trnheader(PLMD::xdrfile::XDRFILE, PLMD::xdrfile::mybool, PLMD::xdrfile::t_trnheader)’: xdrfile_trr.cpp:136:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 136 | if (slen != strlen(version)+1) | if (xdrfile_write_string(const_cast<char*>(version),xd) != (strlen(version)+1) ) | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
|---|
| In file included from xdrfile_xtc.cpp:57: xdrfile_xtc.h:32:2: warning: "/*" within comment [-Wcomment] 32 | / -- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- |
|---|
xdrfile_xtc.cpp: In function ‘int PLMD::xdrfile::xtc_coord(PLMD::xdrfile::XDRFILE, int, float ()[3], float ()[3], float, PLMD::xdrfile::mybool)’:
xdrfile_xtc.cpp:94:13: warning: unused variable ‘i’ [-Wunused-variable]
94 | int i,j,result;
| ^
xdrfile_xtc.cpp:94:15: warning: unused variable ‘j’ [-Wunused-variable]
94 | int i,j,result;
| ^
make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/xdrfile'
compiling MultiColvarBase.cpp
h36.cpp: In function ‘const char PLMD::h36::decode_pure(const int, unsigned int, const char, unsigned int, int)’:
h36.cpp:154:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
154 | if (dv < 0 || dv >= digits_size) {
| ~^~~~
compiling Ghost.cpp
compiling PCARMSD.cpp
compiling ReferenceArguments.cpp
compiling Position.cpp
compiling ReferenceAtoms.cpp
MultiColvarBase.cpp: In member function ‘void PLMD::multicolvar::MultiColvarBase::setupActiveTaskSet(std::vector~~
compiling Pbc.cpp
compiling PDB.cpp
compiling PlumedHandle.cpp
compiling Random.cpp
make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/colvar'
compiling RMSD.cpp
compiling RootFindingBase.cpp
make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/multicolvar'
compiling Stopwatch.cpp
compiling Subprocess.cpp
compiling SwitchingFunction.cpp
compiling Tensor.cpp
compiling Tools.cpp
compiling Torsion.cpp
compiling Tree.cpp
compiling TypesafePtr.cpp
compiling Units.cpp
compiling Vector.cpp
make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/vesselbase'
make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/isdb'
make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/tools'
make[5]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make[4]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make lib
make[4]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
mpic++ -O3 -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/kT.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/pesmd.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/CoordinationBase.o ../colvar/Coordination.o ../colvar/DHEnergy.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/DRMSD.o ../colvar/EEFSolv.o ../colvar/Energy.o ../colvar/ERMSD.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PathMSDBase.o ../colvar/PathMSD.o ../colvar/PCARMSD.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/Action.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GenericMolInfo.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/Caliber.o ../isdb/CS2Backbone.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/MetainferenceBase.o ../isdb/Metainference.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PathBase.o ../mapping/Path.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PCAVars.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/DRMSD.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/RMSDBase.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/h36.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/Pbc.o ../tools/PDB.o ../tools/PlumedHandle.o ../tools/Random.o ../tools/RMSD.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/Config.o ../wrapper/PlumedStatic.o -o plumed-static -ldl -lstdc++ -lgsl -lz -ldl -llapack -lblas -rdynamic -Wl,-Bsymbolic -fopenmp
Building Plumed.inc
chmod a+x plumed-config
chmod a+x plumed-mklib
chmod a+x plumed-newcv
mpic++ -shared -o libplumedKernel.so ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/kT.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/pesmd.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/CoordinationBase.o ../colvar/Coordination.o ../colvar/DHEnergy.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/DRMSD.o ../colvar/EEFSolv.o ../colvar/Energy.o ../colvar/ERMSD.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PathMSDBase.o ../colvar/PathMSD.o ../colvar/PCARMSD.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/Action.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GenericMolInfo.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/Caliber.o ../isdb/CS2Backbone.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/MetainferenceBase.o ../isdb/Metainference.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PathBase.o ../mapping/Path.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PCAVars.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/DRMSD.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/RMSDBase.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/h36.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/Pbc.o ../tools/PDB.o ../tools/PlumedHandle.o ../tools/Random.o ../tools/RMSD.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/Config.o -Wl,-soname,"libplumedKernel.so" -lstdc++ -lgsl -lz -ldl -llapack -lblas -rdynamic -Wl,-Bsymbolic -fopenmp
chmod a+x plumed-partial_tempering
mpic++ -O3 -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/Plumed.o -o plumed-runtime -ldl
ar cr libplumedWrapper.a ../wrapper/Plumed.o
Building Plumed.inc, runtime-linking version
Building Plumed.inc, shared version
chmod a+x plumed-patch
chmod a+x plumed-selector
Building Plumed.inc, static version
Building Plumed.cmake
chmod a+x plumed-vim2html
Building Plumed.cmake, static version
Building Plumed.cmake, runtime-linking version
Building Plumed.cmake, shared version
mpic++ -shared -o libplumed.so ../wrapper/PlumedStatic.o libplumedKernel.so -Wl,-soname,"libplumed.so"
mpic++ -O3 -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/PlumedStatic.o libplumedKernel.so -o plumed -ldl
make[4]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make install-build
make[4]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
mkdir -p install/
make PLUMED_INSTALL=Install all
make[5]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make dirslinks
make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
Updating links to used modules in all directories
make ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links ../xdrfile.links
make[7]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make -C ../analysis links
make -C ../asmjit links
make -C ../bias links
make -C ../blas links
make -C ../cltools links
make -C ../colvar links
make -C ../config links
make -C ../core links
make -C ../function links
make -C ../generic links
make -C ../gridtools links
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/blas'
make -C ../isdb links
make -C ../lapack links
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/blas
make -C ../lepton links
make -C ../main links
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config'
make -C ../mapping links
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/blas'
make -C ../molfile links
Nothing to do in /home/shuvadip/Downloads/plumed-2.9.0/src/config
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lapack'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/main'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/lapack
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/molfile'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/main
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config'
make -C ../multicolvar links
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/bias'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/molfile
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lepton'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/function'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/cltools'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/bias
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/lepton
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/molfile'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/function
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/cltools
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/asmjit'
make -C ../reference links
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/asmjit
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/analysis'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/asmjit'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/isdb'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/analysis
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/isdb
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/mapping'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/generic'
make -C ../secondarystructure links
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/mapping
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/generic
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/core'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/core
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/gridtools'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/secondarystructure'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/gridtools
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/colvar'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lapack'
make -C ../setup links
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/secondarystructure
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/colvar
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/setup'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/setup
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/reference'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/reference
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/multicolvar'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/multicolvar
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/main'
make -C ../tools links
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lepton'
make -C ../vatom links
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/vatom'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/vatom
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/tools'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/tools
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/bias'
make -C ../vesselbase links
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/core'
make -C ../wrapper links
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/wrapper'
Nothing to do in /home/shuvadip/Downloads/plumed-2.9.0/src/wrapper
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/wrapper'
make -C ../xdrfile links
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/xdrfile'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/xdrfile
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/vesselbase'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/xdrfile'
Verify modules and create links in /home/shuvadip/Downloads/plumed-2.9.0/src/vesselbase
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/reference'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/generic'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/setup'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/colvar'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/gridtools'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/function'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/tools'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/cltools'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/vatom'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/isdb'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/secondarystructure'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/mapping'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/multicolvar'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/analysis'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/vesselbase'
make[7]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make dirs
make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
Compiling all directories
make ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper ../xdrfile
make[7]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make -C ../analysis obj
make -C ../asmjit obj
make -C ../bias obj
make -C ../blas obj
make -C ../cltools obj
make -C ../colvar obj
make -C ../config obj
make -C ../core obj
make -C ../function obj
make -C ../generic obj
make -C ../gridtools obj
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/blas'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/blas'
make -C ../isdb obj
make -C ../lapack obj
make -C ../lepton obj
make -C ../main obj
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config'
make PLUMED_FORCE=yes ConfigInstall.inc Config.inc version.h config.txt
make -C ../mapping obj
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lapack'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lapack'
make[9]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config'
make -C ../molfile obj
Updating ConfigInstall.inc
Updating Config.inc
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/main'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/main'
make -C ../multicolvar obj
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lepton'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lepton'
make -C ../reference obj
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/asmjit'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/asmjit'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/molfile'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/molfile'
make -C ../secondarystructure obj
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/bias'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/bias'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/function'
make[8]: Nothing to be done for 'obj'.
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/cltools'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/cltools'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/function'
make -C ../setup obj
make[9]: 'config.txt' is up to date.
Updating version.h
cmp -s Config.inc~ Config.inc || cp Config.inc~ Config.inc
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/generic'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/generic'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/core'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/core'
rm Config.inc~
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/isdb'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/isdb'
make -C ../tools obj
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/analysis'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/analysis'
make -C ../vatom obj
make -C ../vesselbase obj
make -C ../wrapper obj
make -C ../xdrfile obj
cmp -s ConfigInstall.inc~ ConfigInstall.inc || cp ConfigInstall.inc~ ConfigInstall.inc
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/secondarystructure'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/secondarystructure'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/wrapper'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/wrapper'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/mapping'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/mapping'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/xdrfile'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/xdrfile'
rm ConfigInstall.inc~
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/setup'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/setup'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/vatom'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/vatom'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/gridtools'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/gridtools'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/colvar'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/colvar'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/reference'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/reference'
make[9]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config'
make Config.o ConfigInstall.o compile_options.sh
make[9]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config'
make[9]: 'Config.o' is up to date.
make[9]: 'ConfigInstall.o' is up to date.
make[9]: 'compile_options.sh' is up to date.
make[9]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config'
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/config'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/vesselbase'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/vesselbase'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/tools'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/tools'
make[8]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/multicolvar'
make[8]: Nothing to be done for 'obj'.
make[8]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/multicolvar'
make[7]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make lib
make[6]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
mpic++ -O3 -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/kT.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/pesmd.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/CoordinationBase.o ../colvar/Coordination.o ../colvar/DHEnergy.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/DRMSD.o ../colvar/EEFSolv.o ../colvar/Energy.o ../colvar/ERMSD.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PathMSDBase.o ../colvar/PathMSD.o ../colvar/PCARMSD.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/Action.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GenericMolInfo.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/Caliber.o ../isdb/CS2Backbone.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/MetainferenceBase.o ../isdb/Metainference.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PathBase.o ../mapping/Path.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PCAVars.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/DRMSD.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/RMSDBase.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/h36.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/Pbc.o ../tools/PDB.o ../tools/PlumedHandle.o ../tools/Random.o ../tools/RMSD.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/ConfigInstall.o ../wrapper/PlumedStatic.o -o install/plumed-static -ldl -lstdc++ -lgsl -lz -ldl -llapack -lblas -rdynamic -Wl,-Bsymbolic -fopenmp
Building Plumed.inc
chmod a+x install/plumed-config
chmod a+x install/plumed-mklib
chmod a+x install/plumed-newcv
chmod a+x install/plumed-partial_tempering
mkdir -p install
mpic++ -O3 -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/Plumed.o -o install/plumed-runtime -ldl
mpic++ -shared -o install/libplumedKernel.so ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/kT.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/pesmd.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/CoordinationBase.o ../colvar/Coordination.o ../colvar/DHEnergy.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/DRMSD.o ../colvar/EEFSolv.o ../colvar/Energy.o ../colvar/ERMSD.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PathMSDBase.o ../colvar/PathMSD.o ../colvar/PCARMSD.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/Action.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GenericMolInfo.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/Caliber.o ../isdb/CS2Backbone.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/MetainferenceBase.o ../isdb/Metainference.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PathBase.o ../mapping/Path.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PCAVars.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/DRMSD.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/RMSDBase.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/h36.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/Pbc.o ../tools/PDB.o ../tools/PlumedHandle.o ../tools/Random.o ../tools/RMSD.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/ConfigInstall.o -Wl,-soname,"libplumedKernel.so" -lstdc++ -lgsl -lz -ldl -llapack -lblas -rdynamic -Wl,-Bsymbolic -fopenmp
chmod a+x install/plumed-patch
mkdir -p install
ar cr install/libplumedWrapper.a ../wrapper/Plumed.o
chmod a+x install/plumed-selector
Building Plumed.inc, runtime-linking version
Building Plumed.inc, shared version
Building Plumed.inc, static version
chmod a+x install/plumed-vim2html
Building Plumed.cmake
Building Plumed.cmake, static version
Building Plumed.cmake, runtime-linking version
Building Plumed.cmake, shared version
mkdir -p install
mpic++ -O3 -fPIC -Wall -pedantic -std=c++11 ../main/main.o ../wrapper/PlumedStatic.o install/libplumedKernel.so -o install/plumed -ldl
mpic++ -shared -o install/libplumed.so ../wrapper/PlumedStatic.o install/libplumedKernel.so -Wl,-soname,"libplumed.so"
make[6]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make[5]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make PLUMED_INSTALL=Install install/kernel.o
make[5]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
ld -r -o install/kernel.o ../analysis/AnalysisBase.o ../analysis/Average.o ../analysis/AverageVessel.o ../analysis/Committor.o ../analysis/DataCollectionObject.o ../analysis/EuclideanDissimilarityMatrix.o ../analysis/FarthestPointSampling.o ../analysis/Histogram.o ../analysis/LandmarkSelectionBase.o ../analysis/LandmarkStaged.o ../analysis/OutputColvarFile.o ../analysis/OutputPDBFile.o ../analysis/PrintDissimilarityMatrix.o ../analysis/ReadAnalysisFrames.o ../analysis/ReadDissimilarityMatrix.o ../analysis/ReselectLandmarks.o ../analysis/SelectRandomFrames.o ../analysis/SelectWithStride.o ../analysis/WhamHistogram.o ../analysis/WhamWeights.o ../asmjit/arch.o ../asmjit/assembler.o ../asmjit/codebuilder.o ../asmjit/codecompiler.o ../asmjit/codeemitter.o ../asmjit/codeholder.o ../asmjit/constpool.o ../asmjit/cpuinfo.o ../asmjit/func.o ../asmjit/globals.o ../asmjit/inst.o ../asmjit/logging.o ../asmjit/operand.o ../asmjit/osutils.o ../asmjit/regalloc.o ../asmjit/runtime.o ../asmjit/string.o ../asmjit/utils.o ../asmjit/vmem.o ../asmjit/x86assembler.o ../asmjit/x86builder.o ../asmjit/x86compiler.o ../asmjit/x86inst.o ../asmjit/x86instimpl.o ../asmjit/x86internal.o ../asmjit/x86logging.o ../asmjit/x86operand.o ../asmjit/x86operand_regs.o ../asmjit/x86regalloc.o ../asmjit/zone.o ../bias/ABMD.o ../bias/Bias.o ../bias/BiasValue.o ../bias/ExtendedLagrangian.o ../bias/External.o ../bias/LWalls.o ../bias/MaxEnt.o ../bias/MetaD.o ../bias/MovingRestraint.o ../bias/PBMetaD.o ../bias/Restraint.o ../bias/ReweightBase.o ../bias/ReweightBias.o ../bias/ReweightMetad.o ../bias/ReweightTemperaturePressure.o ../bias/ReweightWham.o ../bias/UWalls.o ../blas/blas.o ../cltools/CLTool.o ../cltools/Completion.o ../cltools/Driver.o ../cltools/DriverDouble.o ../cltools/DriverFloat.o ../cltools/GenExample.o ../cltools/GenJson.o ../cltools/GenTemplate.o ../cltools/Info.o ../cltools/kT.o ../cltools/Manual.o ../cltools/PdbRenumber.o ../cltools/pesmd.o ../cltools/SimpleMD.o ../cltools/SumHills.o ../colvar/Angle.o ../colvar/Cell.o ../colvar/Colvar.o ../colvar/Constant.o ../colvar/ContactMap.o ../colvar/CoordinationBase.o ../colvar/Coordination.o ../colvar/DHEnergy.o ../colvar/Dimer.o ../colvar/Dipole.o ../colvar/Distance.o ../colvar/DRMSD.o ../colvar/EEFSolv.o ../colvar/Energy.o ../colvar/ERMSD.o ../colvar/ExtraCV.o ../colvar/Fake.o ../colvar/GHBFIX.o ../colvar/Gyration.o ../colvar/MultiRMSD.o ../colvar/PathMSDBase.o ../colvar/PathMSD.o ../colvar/PCARMSD.o ../colvar/Position.o ../colvar/ProjectionOnAxis.o ../colvar/PropertyMap.o ../colvar/Puckering.o ../colvar/RMSD.o ../colvar/Template.o ../colvar/Torsion.o ../colvar/Volume.o ../core/ActionAnyorder.o ../core/ActionAtomistic.o ../core/Action.o ../core/ActionPilot.o ../core/ActionRegister.o ../core/ActionSet.o ../core/ActionSetup.o ../core/ActionShortcut.o ../core/ActionWithArguments.o ../core/ActionWithValue.o ../core/ActionWithVirtualAtom.o ../core/Atoms.o ../core/CLTool.o ../core/CLToolMain.o ../core/CLToolRegister.o ../core/Colvar.o ../core/DataFetchingObject.o ../core/ExchangePatterns.o ../core/FlexibleBin.o ../core/GenericMolInfo.o ../core/GREX.o ../core/MDAtoms.o ../core/PlumedMain.o ../core/PlumedMainInitializer.o ../core/TargetDist.o ../core/Value.o ../core/WithCmd.o ../function/Combine.o ../function/Custom.o ../function/Ensemble.o ../function/FuncPathGeneral.o ../function/FuncPathMSD.o ../function/FuncSumHills.o ../function/Function.o ../function/LocalEnsemble.o ../function/Piecewise.o ../function/Sort.o ../function/Stats.o ../function/Target.o ../generic/Debug.o ../generic/DumpAtoms.o ../generic/DumpDerivatives.o ../generic/DumpForces.o ../generic/DumpMassCharge.o ../generic/DumpProjections.o ../generic/EffectiveEnergyDrift.o ../generic/EndPlumed.o ../generic/FitToTemplate.o ../generic/Flush.o ../generic/Group.o ../generic/Include.o ../generic/MolInfo.o ../generic/Plumed.o ../generic/Print.o ../generic/RandomExchanges.o ../generic/Read.o ../generic/ResetCell.o ../generic/Time.o ../generic/UpdateIf.o ../generic/WholeMolecules.o ../generic/WrapAround.o ../gridtools/ActionWithGrid.o ../gridtools/ActionWithInputGrid.o ../gridtools/ActionWithIntegral.o ../gridtools/AverageOnGrid.o ../gridtools/ContourFindingBase.o ../gridtools/ConvertToFES.o ../gridtools/DumpCube.o ../gridtools/DumpGrid.o ../gridtools/FindContour.o ../gridtools/FindContourSurface.o ../gridtools/FindSphericalContour.o ../gridtools/FourierTransform.o ../gridtools/GridPrintingBase.o ../gridtools/GridSearch.o ../gridtools/GridToXYZ.o ../gridtools/GridVessel.o ../gridtools/HistogramOnGrid.o ../gridtools/IntegrateGrid.o ../gridtools/InterpolateGrid.o ../isdb/Caliber.o ../isdb/CS2Backbone.o ../isdb/EMMI.o ../isdb/FretEfficiency.o ../isdb/Jcoupling.o ../isdb/MetainferenceBase.o ../isdb/Metainference.o ../isdb/NOE.o ../isdb/PRE.o ../isdb/RDC.o ../isdb/Rescale.o ../isdb/SAXS.o ../isdb/Select.o ../isdb/Selector.o ../lapack/lapack.o ../lepton/CompiledExpression.o ../lepton/ExpressionProgram.o ../lepton/ExpressionTreeNode.o ../lepton/Operation.o ../lepton/ParsedExpression.o ../lepton/Parser.o ../mapping/AdaptivePath.o ../mapping/Mapping.o ../mapping/PathBase.o ../mapping/Path.o ../mapping/PathReparameterization.o ../mapping/PathTools.o ../mapping/PCAVars.o ../mapping/PropertyMap.o ../mapping/SpathVessel.o ../mapping/TrigonometricPathVessel.o ../mapping/ZpathVessel.o ../molfile/crdplugin.o ../molfile/dcdplugin.o ../molfile/gromacsplugin.o ../molfile/pdbplugin.o ../multicolvar/ActionVolume.o ../multicolvar/AlphaBeta.o ../multicolvar/Angles.o ../multicolvar/AtomValuePack.o ../multicolvar/Bridge.o ../multicolvar/BridgedMultiColvarFunction.o ../multicolvar/CatomPack.o ../multicolvar/CenterOfMultiColvar.o ../multicolvar/CoordinationNumbers.o ../multicolvar/Density.o ../multicolvar/DihedralCorrelation.o ../multicolvar/DistanceFromContour.o ../multicolvar/Distances.o ../multicolvar/DumpMultiColvar.o ../multicolvar/FilterBetween.o ../multicolvar/FilterLessThan.o ../multicolvar/FilterMoreThan.o ../multicolvar/InPlaneDistances.o ../multicolvar/LocalAverage.o ../multicolvar/MultiColvarBase.o ../multicolvar/MultiColvarCombine.o ../multicolvar/MultiColvarDensity.o ../multicolvar/MultiColvarFilter.o ../multicolvar/MultiColvarProduct.o ../multicolvar/NumberOfLinks.o ../multicolvar/Torsions.o ../multicolvar/VolumeAround.o ../multicolvar/VolumeBetweenContours.o ../multicolvar/VolumeCavity.o ../multicolvar/VolumeGradientBase.o ../multicolvar/VolumeInCylinder.o ../multicolvar/VolumeInSphere.o ../multicolvar/VolumeTetrapore.o ../multicolvar/XAngle.o ../multicolvar/XDistances.o ../multicolvar/XYDistances.o ../multicolvar/XYTorsion.o ../reference/ArgumentOnlyDistance.o ../reference/Direction.o ../reference/DotProductDistance.o ../reference/DRMSD.o ../reference/EuclideanDistance.o ../reference/FakeFrame.o ../reference/IntermolecularDRMSD.o ../reference/IntramolecularDRMSD.o ../reference/MahalanobisDistance.o ../reference/MetricRegister.o ../reference/MultiDomainRMSD.o ../reference/NormalizedEuclideanDistance.o ../reference/OptimalRMSD.o ../reference/ReferenceArguments.o ../reference/ReferenceAtoms.o ../reference/ReferenceConfiguration.o ../reference/ReferenceValuePack.o ../reference/RMSDBase.o ../reference/SimpleRMSD.o ../reference/SingleDomainRMSD.o ../secondarystructure/AlphaRMSD.o ../secondarystructure/AntibetaRMSD.o ../secondarystructure/ParabetaRMSD.o ../secondarystructure/SecondaryStructureRMSD.o ../setup/Load.o ../setup/Restart.o ../setup/Units.o ../tools/Angle.o ../tools/AtomNumber.o ../tools/BiasRepresentation.o ../tools/Brent1DRootSearch.o ../tools/Citations.o ../tools/Communicator.o ../tools/ConjugateGradient.o ../tools/DLLoader.o ../tools/DynamicList.o ../tools/ERMSD.o ../tools/Exception.o ../tools/FileBase.o ../tools/ForwardDecl.o ../tools/Grid.o ../tools/h36.o ../tools/HistogramBead.o ../tools/IFile.o ../tools/KernelFunctions.o ../tools/Keywords.o ../tools/LatticeReduction.o ../tools/LinkCells.o ../tools/Log.o ../tools/LoopUnroller.o ../tools/Matrix.o ../tools/MatrixSquareBracketsAccess.o ../tools/Minimise1DBrent.o ../tools/MinimiseBase.o ../tools/MolDataClass.o ../tools/MultiValue.o ../tools/NeighborList.o ../tools/OFile.o ../tools/OpenMP.o ../tools/Pbc.o ../tools/PDB.o ../tools/PlumedHandle.o ../tools/Random.o ../tools/RMSD.o ../tools/RootFindingBase.o ../tools/Stopwatch.o ../tools/Subprocess.o ../tools/SwitchingFunction.o ../tools/Tensor.o ../tools/Tools.o ../tools/Torsion.o ../tools/Tree.o ../tools/TypesafePtr.o ../tools/Units.o ../tools/Vector.o ../vatom/ActionWithVirtualAtom.o ../vatom/Center.o ../vatom/FixedAtom.o ../vatom/Ghost.o ../vesselbase/ActionWithAveraging.o ../vesselbase/ActionWithInputVessel.o ../vesselbase/ActionWithVessel.o ../vesselbase/AltMin.o ../vesselbase/AveragingVessel.o ../vesselbase/Between.o ../vesselbase/BridgeVessel.o ../vesselbase/FunctionVessel.o ../vesselbase/Highest.o ../vesselbase/Histogram.o ../vesselbase/LessThan.o ../vesselbase/Lowest.o ../vesselbase/Max.o ../vesselbase/Mean.o ../vesselbase/Min.o ../vesselbase/Moments.o ../vesselbase/MoreThan.o ../vesselbase/OrderingVessel.o ../vesselbase/ShortcutVessel.o ../vesselbase/StoreDataVessel.o ../vesselbase/Sum.o ../vesselbase/ValueVessel.o ../vesselbase/Vessel.o ../vesselbase/VesselRegister.o ../xdrfile/xdrfile.o ../xdrfile/xdrfile_trr.o ../xdrfile/xdrfile_xtc.o ../config/ConfigInstall.o
make[5]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make PLUMED_INSTALL=Install install/libplumed.a
make[5]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
rm -f install/libplumed.a
ar cr install/libplumed.a install/kernel.o ../wrapper/PlumedStatic.o
make[5]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make[4]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make[3]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src/lib'
make[2]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/src'
make[1]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0'
make -C vim
make[1]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/vim'
./vimsyntax.sh
make[1]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/vim'
make -C python
make[1]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/python'
Building python interface for PLUMED
unset CXX && unset CC && unset CFLAGS && unset CXXFLAGS && unset LDSHARED && \
plumed_program_name=plumed \
plumed_force_cython=yes \
plumed_version=2.9.0 \
plumed_include_dir=../src/wrapper \
plumed_default_kernel="$PWD/../src/lib/libplumedKernel.so" \
python setup.py build_ext -i
Module name plumed
Version number 2.9.0
Hardcoded PLUMED_KERNEL /home/shuvadip/Downloads/plumed-2.9.0/src/lib/libplumedKernel.so
plumed_force_cython=yes
importing cython
Compiling plumed.pyx because it changed.
[1/1] Cythonizing plumed.pyx
running build_ext
building 'plumed' extension
creating build
creating build/temp.linux-x86_64-cpython-312
gcc -pthread -B /home/shuvadip/Amber/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/shuvadip/Amber/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/shuvadip/Amber/amber22_src/build/CMakeFiles/miniconda/install/include -fPIC -I../src/wrapper -I/home/shuvadip/Amber/amber22/miniconda/include/python3.12 -c plumed.c -o build/temp.linux-x86_64-cpython-312/plumed.o -DPLUMED_HAS_DLOPEN -DPLUMED_WRAPPER_LINK_RUNTIME=1 -DPLUMED_WRAPPER_IMPLEMENTATION=1 -DPLUMED_WRAPPER_EXTERN=0 -DPLUMED_DEFAULT_KERNEL=/home/shuvadip/Downloads/plumed-2.9.0/src/lib/libplumedKernel.so
plumed.c:35799:20: warning: ‘pyx_mdef_pyx_memoryviewslice_3__setstate_cython’ defined but not used [-Wunused-variable]
35799 | static PyMethodDef pyxmdefpyx_memoryviewslice_3setstate_cython = {"setstate_cython", (PyCFunction)pyxpwpyx_memoryviewslice_3setstate_cython__, METH_O, 0};
| ^~~~~~~~~~~~~
plumed.c:35741:20: warning: ‘pyx_mdef_pyx_memoryviewslice_1__reduce_cython’ defined but not used [-Wunused-variable]
35741 | static PyMethodDef pyxmdefpyx_memoryviewslice_1reduce_cython = {"reduce_cython", (PyCFunction)pyxpwpyx_memoryviewslice_1reduce_cython__, METH_NOARGS, 0};
| ^~~~~~~~~~~
plumed.c:32896:20: warning: ‘pyx_mdef_pyx_memoryview_3__setstate_cython’ defined but not used [-Wunused-variable]
32896 | static PyMethodDef pyxmdefpyx_memoryview_3setstate_cython = {"setstate_cython", (PyCFunction)pyxpwpyx_memoryview_3setstate_cython__, METH_O, 0};
| ^~~~~~~~~~~~
plumed.c:32838:20: warning: ‘pyx_mdef_pyx_memoryview_1__reduce_cython’ defined but not used [-Wunused-variable]
32838 | static PyMethodDef pyxmdefpyx_memoryview_1reduce_cython = {"reduce_cython", (PyCFunction)pyxpwpyx_memoryview_1reduce_cython__, METH_NOARGS, 0};
| ^~~~~~~~~~
plumed.c:32744:20: warning: ‘pyx_mdef_15View_dot_MemoryView_10memoryview_23copy_fortran’ defined but not used [-Wunused-variable]
32744 | static PyMethodDef pyx_mdef_15View_dot_MemoryView_10memoryview_23copy_fortran = {"copy_fortran", (PyCFunction)pyx_memoryview_copy_fortran, METH_NOARGS, 0};
| ^~~~~~~~~~~~~~~~
plumed.c:32649:20: warning: ‘pyx_mdef_15View_dot_MemoryView_10memoryview_21copy’ defined but not used [-Wunused-variable]
32649 | static PyMethodDef pyx_mdef_15View_dot_MemoryView_10memoryview_21copy = {"copy", (PyCFunction)pyx_memoryview_copy, METH_NOARGS, 0};
| ^~~~~~~~~~~~
plumed.c:32572:20: warning: ‘pyx_mdef_15View_dot_MemoryView_10memoryview_19is_f_contig’ defined but not used [-Wunused-variable]
32572 | static PyMethodDef pyx_mdef_15View_dot_MemoryView_10memoryview_19is_f_contig = {"is_f_contig", (PyCFunction)__pyx_memoryview_is_f_contig, METH_NOARGS, 0};
| ^~~~~~~~~~~~~~~
plumed.c:32495:20: warning: ‘pyx_mdef_15View_dot_MemoryView_10memoryview_17is_c_contig’ defined but not used [-Wunused-variable]
32495 | static PyMethodDef pyx_mdef_15View_dot_MemoryView_10memoryview_17is_c_contig = {"is_c_contig", (PyCFunction)pyx_memoryview_is_c_contig, METH_NOARGS, 0};
| ^~~~~~~~~~~~~~~
plumed.c:28603:20: warning: ‘pyxmdefpyx_MemviewEnum_3setstate_cython’ defined but not used [-Wunused-variable]
28603 | static PyMethodDef pyx_mdef_pyx_MemviewEnum_3setstate_cython = {"setstate_cython", (PyCFunction)pyx_pw_pyx_MemviewEnum_3setstate_cython, METH_O, 0};
| ^~~~~~~~~~~~~
plumed.c:28367:20: warning: ‘pyxmdefpyx_MemviewEnum_1reduce_cython’ defined but not used [-Wunused-variable]
28367 | static PyMethodDef pyx_mdef_pyx_MemviewEnum_1reduce_cython = {"reduce_cython", (PyCFunction)pyx_pw_pyx_MemviewEnum_1reduce_cython, METH_NOARGS, 0};
| ^~~~~~~~~~~
plumed.c:27989:20: warning: ‘pyxmdefpyx_array_3setstate_cython’ defined but not used [-Wunused-variable]
27989 | static PyMethodDef pyx_mdef_pyx_array_3setstate_cython = {"setstate_cython", (PyCFunction)pyx_pw_pyx_array_3setstate_cython, METH_O, 0};
| ^~~~~~~~~~~
plumed.c:27931:20: warning: ‘pyxmdefpyx_array_1reduce_cython’ defined but not used [-Wunused-variable]
27931 | static PyMethodDef pyx_mdef_pyx_array_1reduce_cython = {"reduce_cython", (PyCFunction)pyx_pw_pyx_array_1reduce_cython, METH_NOARGS, 0};
| ^~~~~~~~~
creating build/lib.linux-x86_64-cpython-312
gcc -pthread -B /home/shuvadip/Amber/amber22_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/home/shuvadip/Amber/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/shuvadip/Amber/amber22_src/build/CMakeFiles/miniconda/install/lib -L/home/shuvadip/Amber/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/home/shuvadip/Amber/amber22_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/shuvadip/Amber/amber22_src/build/CMakeFiles/miniconda/install/lib -L/home/shuvadip/Amber/amber22_src/build/CMakeFiles/miniconda/install/lib build/temp.linux-x86_64-cpython-312/plumed.o -o build/lib.linux-x86_64-cpython-312/plumed.cpython-312-x86_64-linux-gnu.so
copying build/lib.linux-x86_64-cpython-312/plumed.cpython-312-x86_64-linux-gnu.so ->
make[1]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/python'
LD_LIBRARY_PATH="/home/shuvadip/Downloads/plumed-2.9.0/src/lib":/home/shuvadip/Amber/amber22/lib:/usr/local/gromacs/lib:/home/shuvadip/plumed/lib:/usr/local/cuda-11.8/lib64: PLUMED_PREPEND_PATH="/home/shuvadip/Downloads/plumed-2.9.0/src/lib" make -C json
make[1]: Entering directory '/home/shuvadip/Downloads/plumed-2.9.0/json'
./get_action_list.sh > action_list
../src/lib/plumed --no-mpi gen_json --actions actionlist > syntax.json
make[1]: Leaving directory '/home/shuvadip/Downloads/plumed-2.9.0/json'
GiovanniBussi
debanjansen48
I am trying to install latest version 2.9.0 but encounterd by following error.
According to read me file instruction I installed all dependencies, The error report shown bellow
./configure --prefix=/home/shuvadip/plumed --enable-af_cuda --enable-fftw --enable-python _configure: Optional modules are disabled by default checking for mpic++... mpic++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether mpic++ accepts -g... yes checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gfortran... gfortran checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes configure: Initial CXX: mpic++ configure: Initial CXXFLAGS: -O3 configure: Initial CPPFLAGS:
configure: Initial CFLAGS: -g -O2 configure: Initial LDFLAGS:
configure: Initial LIBS:
configure: Initial STATICLIBS: configure: Initial LD:
configure: Initial LDSHARED: mpic++ configure: Initial SOEXT:
checking whether mpic++ accepts -fPIC... yes checking whether gcc accepts -fPIC... yes checking whether mpic++ accepts -Wall... yes checking whether mpic++ accepts -pedantic... yes checking whether mpic++ accepts -std=c++11... yes checking whether mpic++ declares c++11 support... yes checking whether C++ library supports C++11 exceptions... yes checking whether mpic++ can generate dependency file with -MM -MF... yes configure: dependency tracking enabled configure: Now we will check compulsory headers and libraries checking how to run the C++ preprocessor... mpic++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dirent.h usability... yes checking dirent.h presence... yes checking for dirent.h... yes checking for readdir... yes checking whether dgemv can be linked with no library... no checking whether dgemv can be linked with no library... no checking for library containing dgemv... -lblas checking for library containing dsyevr_... -llapack checking whether sdot returns float... yes configure: Now we will check for optional headers and libraries checking libmolfile_plugin.h usability... no checking libmolfile_plugin.h presence... no checking for libmolfile_plugin.h... no configure: WARNING: cannot enable PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS configure: WARNING: using internal molfile_plugins, which only support dcd/xtc/trr/trj/crd files checking for dlopen in -ldl... yes checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking for library containing MPI_Init... none required checking for mpic++ option to support OpenMP... -fopenmp checking whether architecture is X86/X64... yes checking for library containing clock_gettime... none required configure: Enabling embedded asmjit checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking for library containing regcomp... none required checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for library containing dlopen... none required checking RTLD_DEFAULT without extra libs... yes checking for unistd.h... (cached) yes checking for library containing chdir... none required checking subprocess without extra libs... yes checking for unistd.h... (cached) yes checking for library containing getcwd... none required checking cstdio usability... yes checking cstdio presence... yes checking for cstdio... yes checking for library containing popen... none required checking execinfo.h usability... yes checking execinfo.h presence... yes checking for execinfo.h... yes checking for library containing backtrace... none required checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for library containing gzopen... -lz checking for library containing cblas_dgemv... none required checking gsl/gsl_vector.h usability... yes checking gsl/gsl_vector.h presence... yes checking for gsl/gsl_vector.h... yes checking for library containing gsl_vector_alloc... -lgsl checking fftw3.h usability... no checking fftw3.h presence... no checking for fftw3.h... no configure: WARNING: cannot enable PLUMED_HAS_FFTW checking for python... python configure: Python executable is python checking support for required python modules (python3, setuptools, cython)... yes checking arrayfire.h usability... no checking arrayfire.h presence... no checking for arrayfire.h... no configure: WARNING: cannot enable PLUMED_HAS_ARRAYFIRE checking for arrayfire.h... (cached) no configure: WARNING: cannot enable PLUMED_HAS_ARRAYFIRE_CUDA configure: Release mode, adding -DNDEBUG configure: Special settings for dynamic libraries on Linux configure: Dynamic library extension is 'so' configure: LDSHARED and LDFLAGS need special flags checking whether LDFLAGS can contain -rdynamic... yes checking whether LDFLAGS can contain -Wl,-Bsymbolic... yes configure: Using LDSHARED='mpic++ -shared' configure: Using LDFLAGS=' -rdynamic -Wl,-Bsymbolic' checking whether LDSHARED can create dynamic libraries... yes checking for doxygen... found configure: Doxygen version is fine checking for dot... found configure: Manuals will be generated configure: A PDF version of the manual will not be generated checking whether a program can be run on this machine... yes checking whether a program compiled with mpi can be run on this machine... yes configure: Regtest suite will use env var PLUMED_MPIRUN to run MPI tests (default: mpirun) configure: PLUMED seems to be configured properly! configure: ** checking whether C++ objects can be grouped with ld -r -o... yes checking whether static libraries can be created with ar cr... yes checking whether static-object constructors can be linked from a static archive... yes configure: I will now check if C++ objects can be linked by C/Fortran compilers configure: This is relevant if you want to use plumed patch --static on a non-C++ code checking whether C can link a C++ object... no checking whether C can link a C++ object with library -lstdc++... yes checking whether FORTRAN can link a C++ object... yes checking for pkg-config... /usr/bin/pkg-config configure: bash-completion is not installed or it is installed on a different prefix configure: bash completion for plumed will not be installed configure: PLUMED will be installed using the following paths: configure: prefix: /home/shuvadip/plumed configure: exec_prefix: ${prefix} configure: bindir: ${exec_prefix}/bin configure: libdir: ${exec_prefix}/lib configure: includedir: ${prefix}/include configure: datarootdir: ${prefix}/share configure: datadir: ${datarootdir} configure: docdir: ${prefix}/share/doc/plumed configure: htmldir: ${docdir} configure: Executable will be named plumed configure: As of PLUMED 2.5, you cannot change paths anymore during "make install" configure: Please configure and make clean to change the prefix configure: WARNING: Bash completion for plumed will not be installed, please add the following two lines to your bashrc configure: WARNING: _plumed() { eval "$(plumed --no-mpi completion 2>/dev/null)";} configure: WARNING: complete -F plumed -o default plumed configure: **** PLUMED will be compiled using MPI configure: creating ./config.status config.status: creating Makefile.conf config.status: creating sourceme.sh config.status: creating stamp-h