Closed yurivict closed 6 years ago
jeffhammond
commented
6 years ago Please post the details of the issues you are facing. If you continue to complain without providing any information about the problems you face, I will ignore future requests for support.
jeffhammond
commented
6 years ago Note that FreeBSD support was added in the year 2000 (https://github.com/nwchemgit/nwchem/commit/8d14c6d93ad89b3812bc5e7b5940ce9d376e8a39) and verified in the 4.0 release (https://github.com/nwchemgit/nwchem/blob/master/release.notes.4.0#L251). Any issues with FreeBSD are regressions and thus require the details of what is broken.
edoapra
commented
6 years ago @yurivict Please provide a detailed report of your failure. Please include version of FreeBSD used and MPI libraries used, NWCHEM_TARGET (LINUX64 or LINUX)?
yurivict
commented
6 years ago Note that FreeBSD support was added in the year 2000 (8d14c6d) and verified in the 4.0 release (https://github.com/nwchemgit/nwchem/blob/master/release.notes.4.0#L251). Any issues with FreeBSD are regressions and thus require the details of what is broken.
This is interesting, but it doesn't build on FreeBSD.
Errors are numerous, here is how the error log begins.
gmake[1]: Entering directory '/usr/ports/science/nwchem/work/nwchem-6.8/src'
cat: /usr/ports/science/nwchem/work/nwchem-6.8/src/../src/tools/build/config.h: No such file or directory
gmake -C config -f make_nwchem_config NWCHEM_MODULES="all"
grep: /usr/ports/science/nwchem/work/nwchem-6.8/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8/src/../src/tools/build/Makefile: No such file or directory
gmake[2]: Entering directory '/usr/ports/science/nwchem/work/nwchem-6.8/src/config'
echo \# This configuration generated automatically on \
`hostname` at `date` > nwchem_config.h
echo "# Request modules from user: all" >> nwchem_config.h
echo "NW_MODULE_SUBDIRS = NWints atomscf ddscf gradients moints nwdft rimp2 stepper driver optim cphf ccsd vib mcscf prepar esp hessian selci dplot mp2_grad qhop property solvation nwpw fft analyz nwmd cafe space drdy vscf qmmm qmd etrans tce bq mm cons perfm dntmc dangchang ccca dimqm" >> nwchem_config.h
echo "NW_MODULE_LIBS = -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -ldimqm" >> nwchem_config.h
echo "EXCLUDED_SUBDIRS = develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft" >> nwchem_config.h
echo "CONFIG_LIBS = " >> nwchem_config.h
echo \# This configuration generated automatically on \FreeBSD version: 11.1 amd64
Arguments that are supplied to the build:
MAKE_ENV= NWCHEM_TOP=${WRKSRC}/.. NWCHEM_MODULES=all NWCHEM_LONG_PATHS=Y NWCHEM_TARGET=LINUX64 MPI_INCLUDE=-I${LOCALBASE}/includeMPI used by default is mpich2-1.5_9,5. Other versions are available:
openmp-6.0.0 Open Multi-Processing runtime for LLVM/Clang
openmpi-1.10.7_2 High Performance Message Passing Library
openmpi2-2.1.2_2 High Performance Message Passing LibraryThe bash scripts are all failing on FreeBSD. Please be patient until I found a solution. Thanks
yurivict
commented
6 years ago The bash scripts are all failing on FreeBSD. Please be patient until I found a solution. Thanks
Thanks!
bash is /usr/local/bin/bash on FreeBSD, not /bin/bash as on linux. You can switch to #!/usr/bin/env bash for portability. Otherwise, the syntax is identical.
edoapra
commented
6 years ago Right.
The next hurdle is that expr used FreeBSD is not the one from coreutils (that goes into /usr/local/bin/gexpr)
On 3/26/18 11:13 AM, yuri@FreeBSD wrote:
The bash scripts are all failing on FreeBSD. Please be patient until I found a solution. Thanks
Thanks! bash is /usr/local/bin/bash on FreeBSD, not /bin/bash. You can switch to #!/usr/bin/env bash for portability.
— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/nwchemgit/nwchem/issues/30#issuecomment-376260812, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AE8hodNHkwAOjI2mLlWkGfblERsCbaeyks5tiS-_gaJpZM4S7kFP.
yurivict
commented
6 years ago The next hurdle is that expr used FreeBSD is not the one from coreutils (that goes into /usr/local/bin/gexpr)
/usr/local/bin/gexpr is available from ports: sysutils/coreutils Inside of the FreeBSD port any command can be substituted, ex. expr -> /usr/local/bin/gexpr, with the BINARY_ALIAS command.
edoapra
commented
6 years ago @yurivict I have just pushed a series of changes to the master and hotfix//release-6-8 branches that address the FreeBSD build problems you mentioned. More fixes might be need. Detailed feedback is very welcome
yurivict
commented
6 years ago It wants src/tools/build/config.h:
gmake[1]: Entering directory '/usr/ports/science/nwchem/work/nwchem-dfe8fd8/src'
cat: /usr/ports/science/nwchem/work/nwchem-dfe8fd8/src/../src/tools/build/config.h: No such file or directoryBy providing detailed feedback I mean:
Thanks
yurivict
commented
6 years ago Environment variables:
NWCHEM_TOP=${WRKSRC}/.. NWCHEM_MODULES=all NWCHEM_LONG_PATHS=Y NWCHEM_TARGET=LINUX64 MPI_INCLUDE=-I${LOCALBASE}/include
Steps:
cd src && gmake -f GNUmakefile nwchem_config && \
cd src && gmake -f GNUmakefileOutput:
===> Building for nwchem-6.8
cd /usr/ports/science/nwchem/work/nwchem-dfe8fd8/src && /usr/bin/env NWCHEM_TOP=/usr/ports/science/nwchem/work/nwchem-dfe8fd8/src/.. NWCHEM_MODULES=all NWCHEM_LONG_PATHS=Y NWCHEM_TARGET=LINUX64 MPI_INCLUDE=-I/usr/local/include F77="gfortran6" FC="gfortran6" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc6" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc6" XDG_DATA_HOME=/usr/ports/science/nwchem/work XDG_CONFIG_HOME=/usr/ports/science/nwchem/work HOME=/usr/ports/science/nwchem/work PATH=/usr/ports/science/nwchem/work/.bin:.:/home/yuri/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-omit-frame-pointer -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="-fno-omit-frame-pointer" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -B/usr/local/bin -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-omit-frame-pointer -fstack-protector -fno-strict-aliasing -fno-omit-frame-pointer " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" gmake nwchem_config
gmake[1]: Entering directory '/usr/ports/science/nwchem/work/nwchem-dfe8fd8/src'
cat: /usr/ports/science/nwchem/work/nwchem-dfe8fd8/src/../src/tools/build/config.h: No such file or directory
config/makefile.h:2607: *** missing separator (did you mean TAB instead of 8 spaces?). Stop.
gmake[1]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-dfe8fd8/src'
*** Error code 2Please do not set MPI_INCLUDE. It should be automatically detected. What branch are you using? My suggestion is to use hotfix/release-6-8. Did you set USE_MPI=Y ?
This are the essential env. variables that you should set export NWCHEM_TOP=......../nwchem-6.8.1 export USE_MPI=Y export NWCHEM_TARGET=LINUX64 export USE_INTERNALBLAS=Y export NWCHEM_MODULES=all
edoapra
commented
6 years ago I think I might have found the source of your crash If you confirm that you have been using the master branch, setting USE_INTERNALBLAS=Y should fix it.
yurivict
commented
6 years ago USE_INTERNALBLAS=Y fixed it in master, but not in hotfix/release-6-8:
===> Building for nwchem-6.8
cd /usr/ports/science/nwchem/work/nwchem-e36daf2/src && /usr/bin/env NWCHEM_TOP=/usr/ports/science/nwchem/work/nwchem-e36daf2/src/.. NWCHEM_MODULES=all NWCHEM_LONG_PATHS=Y NWCHEM_TARGET=LINUX64 USE_MPI=Y USE_INTERNALBLAS=Y F77="gfortran6" FC="gfortran6" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc6" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc6" XDG_DATA_HOME=/usr/ports/science/nwchem/work XDG_CONFIG_HOME=/usr/ports/science/nwchem/work HOME=/usr/ports/science/nwchem/work PATH=/usr/ports/science/nwchem/work/.bin:.:/home/yuri/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-omit-frame-pointer -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="-fno-omit-frame-pointer" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -B/usr/local/bin -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-omit-frame-pointer -fstack-protector -fno-strict-aliasing -fno-omit-frame-pointer " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" gmake nwchem_config
gmake[1]: Entering directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src'
cat: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/config.h: No such file or directory
gmake -C config -f make_nwchem_config NWCHEM_MODULES="all"
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
gmake[2]: Entering directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/config'
echo \# This configuration generated automatically on \
`hostname` at `date` > nwchem_config.h
echo "# Request modules from user: all" >> nwchem_config.h
echo "NW_MODULE_SUBDIRS = NWints atomscf ddscf gradients moints nwdft rimp2 stepper driver optim cphf ccsd vib mcscf prepar esp hessian selci dplot mp2_grad qhop property solvation nwpw fft analyz nwmd cafe space drdy vscf qmmm qmd etrans tce bq mm cons perfm dntmc dangchang ccca dimqm" >> nwchem_config.h
echo "NW_MODULE_LIBS = -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -ldimqm" >> nwchem_config.h
echo "EXCLUDED_SUBDIRS = develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft" >> nwchem_config.h
echo "CONFIG_LIBS = " >> nwchem_config.h
echo \# This configuration generated automatically on \
`hostname` at `date` > NWCHEM_CONFIG
echo "# Request modules from user: all" >> NWCHEM_CONFIG
echo The following subdirectories are built: >> NWCHEM_CONFIG
echo NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf >> NWCHEM_CONFIG
echo corresponding to these libraries: >> NWCHEM_CONFIG
echo -lnwints -lanalyze -lguess -lbq -lcafe -lccca -lccsd -lcons -lcphf -ldangchang -lddscf -ldimqm -ldntmc -ldplot -ldrdy -ldriver -lesp -letrans -lpfft -lgradients -lhessian -lmcscf -lmm -lmoints -lmp2 -lnwdft -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -loptim -lperfm -lprepar -lproperty -lqhop -lqmd -lqmmm -lrimp2 -lselci -lsolvation -lspace -lstepper -lnwcutil -ltce -lvib -lvscf >> NWCHEM_CONFIG
echo >> NWCHEM_CONFIG
echo The following directories are excluded from the build: >> NWCHEM_CONFIG
echo develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft >> NWCHEM_CONFIG
echo and these routines will be replaced by stubs: >> NWCHEM_CONFIG
echo argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy >> NWCHEM_CONFIG
echo "No extra configuration libraries were added " >> NWCHEM_CONFIG
cp census.skeleton ../stubs.F
for routine in argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy; do \
sed s/STUBROUTINE/$routine/g stub.skeleton >> ../stubs.F ; \
done
cp util_module_avail_F.begin ../util/util_module_avail.F
echo "c This function was auto generated by make_nwchem_config" >> ../util/util_module_avail.F
for module in NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf; do \
echo " case (\""$module"\")" >> ../util/util_module_avail.F ; \
done
cat util_module_avail_F.end >> ../util/util_module_avail.F
gmake[2]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/config'
gmake -C config -f make_nwchem_config NWCHEM_MODULES="all"
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
gmake[2]: Entering directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/config'
echo \# This configuration generated automatically on \
`hostname` at `date` > nwchem_config.h
echo "# Request modules from user: all" >> nwchem_config.h
echo "NW_MODULE_SUBDIRS = NWints atomscf ddscf gradients moints nwdft rimp2 stepper driver optim cphf ccsd vib mcscf prepar esp hessian selci dplot mp2_grad qhop property solvation nwpw fft analyz nwmd cafe space drdy vscf qmmm qmd etrans tce bq mm cons perfm dntmc dangchang ccca dimqm" >> nwchem_config.h
echo "NW_MODULE_LIBS = -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -ldimqm" >> nwchem_config.h
echo "EXCLUDED_SUBDIRS = develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft" >> nwchem_config.h
echo "CONFIG_LIBS = " >> nwchem_config.h
echo \# This configuration generated automatically on \
`hostname` at `date` > NWCHEM_CONFIG
echo "# Request modules from user: all" >> NWCHEM_CONFIG
echo The following subdirectories are built: >> NWCHEM_CONFIG
echo NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf >> NWCHEM_CONFIG
echo corresponding to these libraries: >> NWCHEM_CONFIG
echo -lnwints -lanalyze -lguess -lbq -lcafe -lccca -lccsd -lcons -lcphf -ldangchang -lddscf -ldimqm -ldntmc -ldplot -ldrdy -ldriver -lesp -letrans -lpfft -lgradients -lhessian -lmcscf -lmm -lmoints -lmp2 -lnwdft -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -loptim -lperfm -lprepar -lproperty -lqhop -lqmd -lqmmm -lrimp2 -lselci -lsolvation -lspace -lstepper -lnwcutil -ltce -lvib -lvscf >> NWCHEM_CONFIG
echo >> NWCHEM_CONFIG
echo The following directories are excluded from the build: >> NWCHEM_CONFIG
echo develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft >> NWCHEM_CONFIG
echo and these routines will be replaced by stubs: >> NWCHEM_CONFIG
echo argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy >> NWCHEM_CONFIG
echo "No extra configuration libraries were added " >> NWCHEM_CONFIG
cp census.skeleton ../stubs.F
for routine in argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy; do \
sed s/STUBROUTINE/$routine/g stub.skeleton >> ../stubs.F ; \
done
cp util_module_avail_F.begin ../util/util_module_avail.F
echo "c This function was auto generated by make_nwchem_config" >> ../util/util_module_avail.F
for module in NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf; do \
echo " case (\""$module"\")" >> ../util/util_module_avail.F ; \
done
cat util_module_avail_F.end >> ../util/util_module_avail.F
gmake[2]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/config'
gmake[1]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src'
gmake[1]: Entering directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src'
cat: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/config.h: No such file or directory
gmake -C config -f make_nwchem_config NWCHEM_MODULES="all"
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
gmake[2]: Entering directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/config'
echo \# This configuration generated automatically on \
`hostname` at `date` > nwchem_config.h
echo \# This configuration generated automatically on \
`hostname` at `date` > NWCHEM_CONFIG
cp census.skeleton ../stubs.F
cp util_module_avail_F.begin ../util/util_module_avail.F
for routine in argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy; do \
sed s/STUBROUTINE/$routine/g stub.skeleton >> ../stubs.F ; \
done
echo "c This function was auto generated by make_nwchem_config" >> ../util/util_module_avail.F
for module in NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf; do \
echo " case (\""$module"\")" >> ../util/util_module_avail.F ; \
done
echo "# Request modules from user: all" >> nwchem_config.h
echo "# Request modules from user: all" >> NWCHEM_CONFIG
echo "NW_MODULE_SUBDIRS = NWints atomscf ddscf gradients moints nwdft rimp2 stepper driver optim cphf ccsd vib mcscf prepar esp hessian selci dplot mp2_grad qhop property solvation nwpw fft analyz nwmd cafe space drdy vscf qmmm qmd etrans tce bq mm cons perfm dntmc dangchang ccca dimqm" >> nwchem_config.h
echo The following subdirectories are built: >> NWCHEM_CONFIG
cat util_module_avail_F.end >> ../util/util_module_avail.F
echo "NW_MODULE_LIBS = -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -ldimqm" >> nwchem_config.h
echo NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf >> NWCHEM_CONFIG
echo "EXCLUDED_SUBDIRS = develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft" >> nwchem_config.h
echo corresponding to these libraries: >> NWCHEM_CONFIG
echo "CONFIG_LIBS = " >> nwchem_config.h
echo -lnwints -lanalyze -lguess -lbq -lcafe -lccca -lccsd -lcons -lcphf -ldangchang -lddscf -ldimqm -ldntmc -ldplot -ldrdy -ldriver -lesp -letrans -lpfft -lgradients -lhessian -lmcscf -lmm -lmoints -lmp2 -lnwdft -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -loptim -lperfm -lprepar -lproperty -lqhop -lqmd -lqmmm -lrimp2 -lselci -lsolvation -lspace -lstepper -lnwcutil -ltce -lvib -lvscf >> NWCHEM_CONFIG
echo >> NWCHEM_CONFIG
echo The following directories are excluded from the build: >> NWCHEM_CONFIG
echo develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft >> NWCHEM_CONFIG
echo and these routines will be replaced by stubs: >> NWCHEM_CONFIG
echo argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy >> NWCHEM_CONFIG
echo "No extra configuration libraries were added " >> NWCHEM_CONFIG
gmake[2]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/config'
test \! -f 64_to_32 -o \! -f 32_to_64 || rm -f 64_to_32 32_to_64
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
test -d /usr/ports/science/nwchem/work/nwchem-e36daf2/src/..-6.8.1/lib/LINUX64 || mkdir -p /usr/ports/science/nwchem/work/nwchem-e36daf2/src/..-6.8.1/lib/LINUX64
test -d /usr/ports/science/nwchem/work/nwchem-e36daf2/src/..-6.8.1/bin/LINUX64 || mkdir -p /usr/ports/science/nwchem/work/nwchem-e36daf2/src/..-6.8.1/bin/LINUX64
./util/util_nwchem_version.bash
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
fatal: Not a git repository (or any parent up to mount point /usr)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Making libraries in tools
gmake[2]: Entering directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/tools'
cat: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/config.h: No such file or directory
../config/makefile.h:141: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/..-6.8.1/src/config/nwchem_config.h: No such file or directory
gmake[2]: *** No rule to make target '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/..-6.8.1/src/config/nwchem_config.h'. Stop.
gmake[2]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/tools'
gmake[1]: *** [GNUmakefile:103: libraries] Error 1
gmake[1]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src'I actually want to use pre-installed blas. In master, it downloads "ga". I also have it pre-installed.
yurivict
commented
6 years ago Here is the current version of the port: https://reviews.freebsd.org/D14857
edoapra
commented
6 years ago edoapra
commented
6 years ago @yurivict my initial comment on the FreeBSD port: Please do not use the master branch since it contains experimental/untested features (please do not start another flam thread on this development style not following strict FOSS guidelines ...) Therefore, please use the most stable branch at this time, e.g. hotfix/release-6-8
yurivict
commented
6 years ago Master revision 1ef1736 tries to download ga-5.6.4.tar.gz. I have it installed.
yurivict
commented
6 years ago please do not start another flam thread
I am not starting any flame threads. I am just saying what I observe.
Revision e36daf2 from hotfix fails:
===> Building for nwchem-6.8
cd /usr/ports/science/nwchem/work/nwchem-e36daf2/src && /usr/bin/env NWCHEM_TOP=/usr/ports/science/nwchem/work/nwchem-e36daf2/src/.. NWCHEM_MODULES=all NWCHEM_LONG_PATHS=Y NWCHEM_TARGET=LINUX64 USE_MPI=Y USE_INTERNALBLAS=Y F77="gfortran6" FC="gfortran6" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc6" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc6" XDG_DATA_HOME=/usr/ports/science/nwchem/work XDG_CONFIG_HOME=/usr/ports/science/nwchem/work HOME=/usr/ports/science/nwchem/work PATH=/usr/ports/science/nwchem/work/.bin:.:/home/yuri/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-omit-frame-pointer -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="-fno-omit-frame-pointer" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -B/usr/local/bin -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-omit-frame-pointer -fstack-protector -fno-strict-aliasing -fno-omit-frame-pointer " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" gmake nwchem_config
gmake[1]: Entering directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src'
cat: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/config.h: No such file or directory
gmake -C config -f make_nwchem_config NWCHEM_MODULES="all"
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
gmake[2]: Entering directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/config'
echo \# This configuration generated automatically on \
`hostname` at `date` > nwchem_config.h
echo "# Request modules from user: all" >> nwchem_config.h
echo "NW_MODULE_SUBDIRS = NWints atomscf ddscf gradients moints nwdft rimp2 stepper driver optim cphf ccsd vib mcscf prepar esp hessian selci dplot mp2_grad qhop property solvation nwpw fft analyz nwmd cafe space drdy vscf qmmm qmd etrans tce bq mm cons perfm dntmc dangchang ccca dimqm" >> nwchem_config.h
echo "NW_MODULE_LIBS = -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -ldimqm" >> nwchem_config.h
echo "EXCLUDED_SUBDIRS = develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft" >> nwchem_config.h
echo "CONFIG_LIBS = " >> nwchem_config.h
echo \# This configuration generated automatically on \
`hostname` at `date` > NWCHEM_CONFIG
echo "# Request modules from user: all" >> NWCHEM_CONFIG
echo The following subdirectories are built: >> NWCHEM_CONFIG
echo NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf >> NWCHEM_CONFIG
echo corresponding to these libraries: >> NWCHEM_CONFIG
echo -lnwints -lanalyze -lguess -lbq -lcafe -lccca -lccsd -lcons -lcphf -ldangchang -lddscf -ldimqm -ldntmc -ldplot -ldrdy -ldriver -lesp -letrans -lpfft -lgradients -lhessian -lmcscf -lmm -lmoints -lmp2 -lnwdft -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -loptim -lperfm -lprepar -lproperty -lqhop -lqmd -lqmmm -lrimp2 -lselci -lsolvation -lspace -lstepper -lnwcutil -ltce -lvib -lvscf >> NWCHEM_CONFIG
echo >> NWCHEM_CONFIG
echo The following directories are excluded from the build: >> NWCHEM_CONFIG
echo develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft >> NWCHEM_CONFIG
echo and these routines will be replaced by stubs: >> NWCHEM_CONFIG
echo argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy >> NWCHEM_CONFIG
echo "No extra configuration libraries were added " >> NWCHEM_CONFIG
cp census.skeleton ../stubs.F
for routine in argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy; do \
sed s/STUBROUTINE/$routine/g stub.skeleton >> ../stubs.F ; \
done
cp util_module_avail_F.begin ../util/util_module_avail.F
echo "c This function was auto generated by make_nwchem_config" >> ../util/util_module_avail.F
for module in NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf; do \
echo " case (\""$module"\")" >> ../util/util_module_avail.F ; \
done
cat util_module_avail_F.end >> ../util/util_module_avail.F
gmake[2]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/config'
gmake -C config -f make_nwchem_config NWCHEM_MODULES="all"
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
gmake[2]: Entering directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/config'
echo \# This configuration generated automatically on \
`hostname` at `date` > nwchem_config.h
echo "# Request modules from user: all" >> nwchem_config.h
echo "NW_MODULE_SUBDIRS = NWints atomscf ddscf gradients moints nwdft rimp2 stepper driver optim cphf ccsd vib mcscf prepar esp hessian selci dplot mp2_grad qhop property solvation nwpw fft analyz nwmd cafe space drdy vscf qmmm qmd etrans tce bq mm cons perfm dntmc dangchang ccca dimqm" >> nwchem_config.h
echo "NW_MODULE_LIBS = -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -ldimqm" >> nwchem_config.h
echo "EXCLUDED_SUBDIRS = develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft" >> nwchem_config.h
echo "CONFIG_LIBS = " >> nwchem_config.h
echo \# This configuration generated automatically on \
`hostname` at `date` > NWCHEM_CONFIG
echo "# Request modules from user: all" >> NWCHEM_CONFIG
echo The following subdirectories are built: >> NWCHEM_CONFIG
echo NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf >> NWCHEM_CONFIG
echo corresponding to these libraries: >> NWCHEM_CONFIG
echo -lnwints -lanalyze -lguess -lbq -lcafe -lccca -lccsd -lcons -lcphf -ldangchang -lddscf -ldimqm -ldntmc -ldplot -ldrdy -ldriver -lesp -letrans -lpfft -lgradients -lhessian -lmcscf -lmm -lmoints -lmp2 -lnwdft -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -loptim -lperfm -lprepar -lproperty -lqhop -lqmd -lqmmm -lrimp2 -lselci -lsolvation -lspace -lstepper -lnwcutil -ltce -lvib -lvscf >> NWCHEM_CONFIG
echo >> NWCHEM_CONFIG
echo The following directories are excluded from the build: >> NWCHEM_CONFIG
echo develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft >> NWCHEM_CONFIG
echo and these routines will be replaced by stubs: >> NWCHEM_CONFIG
echo argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy >> NWCHEM_CONFIG
echo "No extra configuration libraries were added " >> NWCHEM_CONFIG
cp census.skeleton ../stubs.F
for routine in argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy; do \
sed s/STUBROUTINE/$routine/g stub.skeleton >> ../stubs.F ; \
done
cp util_module_avail_F.begin ../util/util_module_avail.F
echo "c This function was auto generated by make_nwchem_config" >> ../util/util_module_avail.F
for module in NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf; do \
echo " case (\""$module"\")" >> ../util/util_module_avail.F ; \
done
cat util_module_avail_F.end >> ../util/util_module_avail.F
gmake[2]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/config'
gmake[1]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src'
gmake[1]: Entering directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src'
cat: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/config.h: No such file or directory
gmake -C config -f make_nwchem_config NWCHEM_MODULES="all"
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
gmake[2]: Entering directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/config'
echo \# This configuration generated automatically on \
`hostname` at `date` > nwchem_config.h
echo \# This configuration generated automatically on \
`hostname` at `date` > NWCHEM_CONFIG
cp census.skeleton ../stubs.F
cp util_module_avail_F.begin ../util/util_module_avail.F
for routine in argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy; do \
sed s/STUBROUTINE/$routine/g stub.skeleton >> ../stubs.F ; \
done
echo "c This function was auto generated by make_nwchem_config" >> ../util/util_module_avail.F
for module in NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf; do \
echo " case (\""$module"\")" >> ../util/util_module_avail.F ; \
done
echo "# Request modules from user: all" >> nwchem_config.h
echo "# Request modules from user: all" >> NWCHEM_CONFIG
echo "NW_MODULE_SUBDIRS = NWints atomscf ddscf gradients moints nwdft rimp2 stepper driver optim cphf ccsd vib mcscf prepar esp hessian selci dplot mp2_grad qhop property solvation nwpw fft analyz nwmd cafe space drdy vscf qmmm qmd etrans tce bq mm cons perfm dntmc dangchang ccca dimqm" >> nwchem_config.h
echo The following subdirectories are built: >> NWCHEM_CONFIG
cat util_module_avail_F.end >> ../util/util_module_avail.F
echo "NW_MODULE_LIBS = -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -ldimqm" >> nwchem_config.h
echo NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf >> NWCHEM_CONFIG
echo "EXCLUDED_SUBDIRS = develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft" >> nwchem_config.h
echo corresponding to these libraries: >> NWCHEM_CONFIG
echo "CONFIG_LIBS = " >> nwchem_config.h
echo -lnwints -lanalyze -lguess -lbq -lcafe -lccca -lccsd -lcons -lcphf -ldangchang -lddscf -ldimqm -ldntmc -ldplot -ldrdy -ldriver -lesp -letrans -lpfft -lgradients -lhessian -lmcscf -lmm -lmoints -lmp2 -lnwdft -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -loptim -lperfm -lprepar -lproperty -lqhop -lqmd -lqmmm -lrimp2 -lselci -lsolvation -lspace -lstepper -lnwcutil -ltce -lvib -lvscf >> NWCHEM_CONFIG
echo >> NWCHEM_CONFIG
echo The following directories are excluded from the build: >> NWCHEM_CONFIG
echo develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft >> NWCHEM_CONFIG
echo and these routines will be replaced by stubs: >> NWCHEM_CONFIG
echo argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy >> NWCHEM_CONFIG
echo "No extra configuration libraries were added " >> NWCHEM_CONFIG
gmake[2]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/config'
test \! -f 64_to_32 -o \! -f 32_to_64 || rm -f 64_to_32 32_to_64
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
test -d /usr/ports/science/nwchem/work/nwchem-e36daf2/src/..-6.8.1/lib/LINUX64 || mkdir -p /usr/ports/science/nwchem/work/nwchem-e36daf2/src/..-6.8.1/lib/LINUX64
test -d /usr/ports/science/nwchem/work/nwchem-e36daf2/src/..-6.8.1/bin/LINUX64 || mkdir -p /usr/ports/science/nwchem/work/nwchem-e36daf2/src/..-6.8.1/bin/LINUX64
./util/util_nwchem_version.bash
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/Makefile: No such file or directory
fatal: Not a git repository (or any parent up to mount point /usr)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Making libraries in tools
gmake[2]: Entering directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/tools'
cat: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/../src/tools/build/config.h: No such file or directory
../config/makefile.h:141: /usr/ports/science/nwchem/work/nwchem-e36daf2/src/..-6.8.1/src/config/nwchem_config.h: No such file or directory
gmake[2]: *** No rule to make target '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/..-6.8.1/src/config/nwchem_config.h'. Stop.
gmake[2]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src/tools'
gmake[1]: *** [GNUmakefile:103: libraries] Error 1
gmake[1]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-e36daf2/src'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1@yurivict I am not quite sure you have read the last comments I made. I will repeat/rephrase them just in case github made them disappear on your end
yurivict
commented
6 years ago Now it fails down again (revision e36daf2 from hotfix/):
===> Building for nwchem-6.8.1
cd /usr/ports/science/nwchem/work/nwchem-6.8.1/src && /usr/bin/env NWCHEM_TOP=/usr/ports/science/nwchem/work/nwchem-6.8.1/src/.. NWCHEM_MODULES=all NWCHEM_LONG_PATHS=Y NWCHEM_TARGET=LINUX64 USE_MPI=Y USE_INTERNALBLAS=Y F77="gfortran6" FC="gfortran6" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc6" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc6" XDG_DATA_HOME=/usr/ports/science/nwchem/work XDG_CONFIG_HOME=/usr/ports/science/nwchem/work HOME=/usr/ports/science/nwchem/work PATH=/usr/ports/science/nwchem/work/.bin:.:/home/yuri/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-omit-frame-pointer -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="-fno-omit-frame-pointer" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -B/usr/local/bin -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-omit-frame-pointer -fstack-protector -fno-strict-aliasing -fno-omit-frame-pointer " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" gmake nwchem_config
gmake[1]: Entering directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src'
cat: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/config.h: No such file or directory
gmake -C config -f make_nwchem_config NWCHEM_MODULES="all"
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
gmake[2]: Entering directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src/config'
echo \# This configuration generated automatically on \
`hostname` at `date` > nwchem_config.h
echo "# Request modules from user: all" >> nwchem_config.h
echo "NW_MODULE_SUBDIRS = NWints atomscf ddscf gradients moints nwdft rimp2 stepper driver optim cphf ccsd vib mcscf prepar esp hessian selci dplot mp2_grad qhop property solvation nwpw fft analyz nwmd cafe space drdy vscf qmmm qmd etrans tce bq mm cons perfm dntmc dangchang ccca dimqm" >> nwchem_config.h
echo "NW_MODULE_LIBS = -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -ldimqm" >> nwchem_config.h
echo "EXCLUDED_SUBDIRS = develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft" >> nwchem_config.h
echo "CONFIG_LIBS = " >> nwchem_config.h
echo \# This configuration generated automatically on \
`hostname` at `date` > NWCHEM_CONFIG
echo "# Request modules from user: all" >> NWCHEM_CONFIG
echo The following subdirectories are built: >> NWCHEM_CONFIG
echo NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf >> NWCHEM_CONFIG
echo corresponding to these libraries: >> NWCHEM_CONFIG
echo -lnwints -lanalyze -lguess -lbq -lcafe -lccca -lccsd -lcons -lcphf -ldangchang -lddscf -ldimqm -ldntmc -ldplot -ldrdy -ldriver -lesp -letrans -lpfft -lgradients -lhessian -lmcscf -lmm -lmoints -lmp2 -lnwdft -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -loptim -lperfm -lprepar -lproperty -lqhop -lqmd -lqmmm -lrimp2 -lselci -lsolvation -lspace -lstepper -lnwcutil -ltce -lvib -lvscf >> NWCHEM_CONFIG
echo >> NWCHEM_CONFIG
echo The following directories are excluded from the build: >> NWCHEM_CONFIG
echo develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft >> NWCHEM_CONFIG
echo and these routines will be replaced by stubs: >> NWCHEM_CONFIG
echo argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy >> NWCHEM_CONFIG
echo "No extra configuration libraries were added " >> NWCHEM_CONFIG
cp census.skeleton ../stubs.F
for routine in argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy; do \
sed s/STUBROUTINE/$routine/g stub.skeleton >> ../stubs.F ; \
done
cp util_module_avail_F.begin ../util/util_module_avail.F
echo "c This function was auto generated by make_nwchem_config" >> ../util/util_module_avail.F
for module in NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf; do \
echo " case (\""$module"\")" >> ../util/util_module_avail.F ; \
done
cat util_module_avail_F.end >> ../util/util_module_avail.F
gmake[2]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src/config'
cat: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/config.h: No such file or directory
gmake -C config -f make_nwchem_config NWCHEM_MODULES="all"
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
gmake[2]: Entering directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src/config'
echo \# This configuration generated automatically on \
`hostname` at `date` > nwchem_config.h
echo "# Request modules from user: all" >> nwchem_config.h
echo "NW_MODULE_SUBDIRS = NWints atomscf ddscf gradients moints nwdft rimp2 stepper driver optim cphf ccsd vib mcscf prepar esp hessian selci dplot mp2_grad qhop property solvation nwpw fft analyz nwmd cafe space drdy vscf qmmm qmd etrans tce bq mm cons perfm dntmc dangchang ccca dimqm" >> nwchem_config.h
echo "NW_MODULE_LIBS = -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -ldimqm" >> nwchem_config.h
echo "EXCLUDED_SUBDIRS = develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft" >> nwchem_config.h
echo "CONFIG_LIBS = " >> nwchem_config.h
echo \# This configuration generated automatically on \
`hostname` at `date` > NWCHEM_CONFIG
echo "# Request modules from user: all" >> NWCHEM_CONFIG
echo The following subdirectories are built: >> NWCHEM_CONFIG
echo NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf >> NWCHEM_CONFIG
echo corresponding to these libraries: >> NWCHEM_CONFIG
echo -lnwints -lanalyze -lguess -lbq -lcafe -lccca -lccsd -lcons -lcphf -ldangchang -lddscf -ldimqm -ldntmc -ldplot -ldrdy -ldriver -lesp -letrans -lpfft -lgradients -lhessian -lmcscf -lmm -lmoints -lmp2 -lnwdft -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -loptim -lperfm -lprepar -lproperty -lqhop -lqmd -lqmmm -lrimp2 -lselci -lsolvation -lspace -lstepper -lnwcutil -ltce -lvib -lvscf >> NWCHEM_CONFIG
echo >> NWCHEM_CONFIG
echo The following directories are excluded from the build: >> NWCHEM_CONFIG
echo develop nwxc scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia rdmft >> NWCHEM_CONFIG
echo and these routines will be replaced by stubs: >> NWCHEM_CONFIG
echo argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy >> NWCHEM_CONFIG
echo "No extra configuration libraries were added " >> NWCHEM_CONFIG
cp census.skeleton ../stubs.F
for routine in argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input nwxc_eval_df nwxc_eval_df2 nwxc_eval_df3 nwxc_get_cam nwxc_get_disp nwxc_getvals nwxc_getwght nwxc_has_2nd nwxc_has_cam nwxc_has_disp nwxc_has_hfx nwxc_has_mp2c nwxc_has_xc nwxc_init nwxc_input nwxc_is_gga nwxc_is_lda nwxc_is_mgga nwxc_is_on nwxc_print nwxc_print_nwpw nwxc_reset_rho_tolerance nwxc_rtdb_delete nwxc_rtdb_load nwxc_rtdb_store nwxc_vdw3_dftd3 nwxc_wght_hfx nwxc_wght_mp2c python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand wfn1_input wfn1_task_energy; do \
sed s/STUBROUTINE/$routine/g stub.skeleton >> ../stubs.F ; \
done
cp util_module_avail_F.begin ../util/util_module_avail.F
echo "c This function was auto generated by make_nwchem_config" >> ../util/util_module_avail.F
for module in NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dimqm dntmc dplot drdy driver esp etrans fft gradients hessian mcscf mm moints mp2_grad nwdft nwmd nwpw optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf; do \
echo " case (\""$module"\")" >> ../util/util_module_avail.F ; \
done
cat util_module_avail_F.end >> ../util/util_module_avail.F
gmake[2]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src/config'
gmake[1]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src'
gmake[1]: Entering directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src'
cat: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/config.h: No such file or directory
test \! -f 64_to_32 -o \! -f 32_to_64 || rm -f 64_to_32 32_to_64
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
test -d /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../lib/LINUX64 || mkdir -p /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../lib/LINUX64
test -d /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../bin/LINUX64 || mkdir -p /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../bin/LINUX64
./util/util_nwchem_version.bash
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
fatal: Not a git repository (or any parent up to mount point /usr)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Making libraries in tools
gmake[2]: Entering directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src/tools'
cat: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/config.h: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
rm -f ./*.FC.stamp
No Global Arrays found: Attempting running ./get-tools
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
./get-tools-github
downloading ga-5.6.4.tar.gz from https://github.com/GlobalArrays/ga/releases/download/v5.6.4/ga-5.6.4.tar.gz
--2018-03-26 13:45:27-- https://github.com/GlobalArrays/ga/releases/download/v5.6.4/ga-5.6.4.tar.gz
Resolving github.com (github.com)... 192.30.255.113, 192.30.255.112
Connecting to github.com (github.com)|192.30.255.113|:443... connected.
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
rm -f ./*.CC.stamp
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
echo "" > gfortran6.FC.stamp
HTTP request sent, awaiting response... grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
rm -rf build install
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
echo "" > cc.CC.stamp
302 Found
Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/82336637/6fc9acfe-2cf5-11e8-9d8c-64e3cd7ea303?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180326%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180326T204527Z&X-Amz-Expires=300&X-Amz-Signature=6c31a0cd1e845160490b1f73ce2665a7e217ff24e932783880416a4b57fdef76&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dga-5.6.4.tar.gz&response-content-type=application%2Foctet-stream [following]
--2018-03-26 13:45:27-- https://github-production-release-asset-2e65be.s3.amazonaws.com/82336637/6fc9acfe-2cf5-11e8-9d8c-64e3cd7ea303?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180326%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180326T204527Z&X-Amz-Expires=300&X-Amz-Signature=6c31a0cd1e845160490b1f73ce2665a7e217ff24e932783880416a4b57fdef76&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dga-5.6.4.tar.gz&response-content-type=application%2Foctet-stream
Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 54.231.72.163
Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|54.231.72.163|:443... grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
rm -f ./*.DIR.stamp
echo "" > ga-5.6.4.MPI-TS.DIR.stamp
connected.
HTTP request sent, awaiting response... 200 OK
Length: 8233112 (7.9M) [application/octet-stream]
Saving to: 'ga-5.6.4.tar.gz'
0K .......... .......... .......... .......... .......... 0% 293K 27s
50K .......... .......... .......... .......... .......... 1% 307K 26s
8000K .......... .......... .......... .......... 100% 13.0M=2.9s
2018-03-26 13:45:30 (2.70 MB/s) - 'ga-5.6.4.tar.gz' saved [8233112/8233112]
x ga-5.6.4/
x ga-5.6.4/compat/
configure present. no autogen.sh required
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
No Global Arrays found: Attempting running ./get-tools
./get-tools-github
configure present. no autogen.sh required
touch ga-5.6.4/configure
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
*** Configuring Parallel Tools ****
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directory
No Global Arrays found: Attempting running ./get-tools
./get-tools-github
../ga-5.6.4/configure --prefix=/usr/ports/science/nwchem/work/nwchem-6.8.1/src/tools/install --with-tcgmsg --with-mpi=-I/usr/local/include -I/usr/local/include -L/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -L/usr/local/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc6 -lpthread -lexecinfo -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -B/usr/local/bin -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -I/usr/local/include -I/usr/local/include -L/usr/local/lib -lmpichf90 -Wl,-rpath -Wl,/usr/local/lib -lmpich -lopa -lmpl -lpthread -L/usr/local/lib --enable-peigs --enable-underscoring --disable-mpi-tests --without-scalapack --without-lapack --without-blas --with-mpi-ts CC=cc CXX=c++ F77=gfortran6 CFLAGS=-fPIC ARMCI_DEFAULT_SHMMAX_UBOUND=131072
configure present. no autogen.sh required
touch ga-5.6.4/armci/Makefile.in
checking build system type... x86_64-unknown-freebsd11.1
checking host system type... x86_64-unknown-freebsd11.1
checking for TARGET base (64bit-ness checked later)... UNKNOWN
checking whether we think this system is what we call SYSV... no
checking whether we are cross compiling... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/local/bin/gmkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
configure: Detected VPATH build
configure:
configure: C compiler
configure:
checking for style of include used by make... GNU
checking whether the C compiler works... no
configure: error: in `/usr/ports/science/nwchem/work/nwchem-6.8.1/src/tools/build':
configure: error: C compiler cannot create executables
See `config.log' for more details
gmake[2]: *** [GNUmakefile:665: build/config.status] Error 1
gmake[2]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src/tools'
gmake[1]: *** [GNUmakefile:103: libraries] Error 1
gmake[1]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/science/nwchemI see that it fails in ga. Like I said, I have it installed:
$ pkg info | grep ^ga-
ga-5.6.4 Partitioned Global Address Space (PGAS) library for distributed arrays
$ pkg info -l ga
ga-5.6.4:
/usr/local/bin/adjust.x
/usr/local/bin/armci-config
/usr/local/bin/collisions.x
/usr/local/bin/comex-config
/usr/local/bin/ga-config
/usr/local/include/armci.h
/usr/local/include/chemio.h
/usr/local/include/comex.h
/usr/local/include/coms.h
/usr/local/include/dra.fh
/usr/local/include/dra.h
/usr/local/include/eaf.fh
/usr/local/include/eaf.h
/usr/local/include/elio.h
/usr/local/include/error.h
/usr/local/include/farg.h
/usr/local/include/ga-mpi.fh
/usr/local/include/ga-mpi.h
/usr/local/include/ga-papi.h
/usr/local/include/ga-wapi.h
/usr/local/include/ga.h
/usr/local/include/gacommon.h
/usr/local/include/global.fh
/usr/local/include/macdecls.h
/usr/local/include/macommon.h
/usr/local/include/maf2c.fh
/usr/local/include/mafdecls.fh
/usr/local/include/matypes.h
/usr/local/include/message.h
/usr/local/include/msgtypesc.h
/usr/local/include/msgtypesf.h
/usr/local/include/parmci.h
/usr/local/include/scope.h
/usr/local/include/sf.fh
/usr/local/include/sf.h
/usr/local/include/string-util.h
/usr/local/include/table.h
/usr/local/include/tcgmsg.fh
/usr/local/include/tcgmsg.h
/usr/local/include/typesf2c.h
/usr/local/lib/libarmci.so
/usr/local/lib/libarmci.so.0
/usr/local/lib/libarmci.so.0.0.0
/usr/local/lib/libcomex.so
/usr/local/lib/libcomex.so.0
/usr/local/lib/libcomex.so.0.0.0
/usr/local/lib/libga.so
/usr/local/lib/libga.so.1
/usr/local/lib/libga.so.1.0.4
/usr/local/share/licenses/ga-5.6.4/BSD3CLAUSE
/usr/local/share/licenses/ga-5.6.4/LICENSE
/usr/local/share/licenses/ga-5.6.4/catalog.mk@yurivict could you please stop pestering me with the story of the external GA library? I would like to get you a working environment for compiling NWChem and the tools compilation is extremely useful to iron out any problem. As I have ALREADY TOLD you several times, will try to provide a way to do to support external GA libraries but this is pretty low on my priorities. If you would like to get NWChem compiled and you are willing to collaborate with me, please follow my suggestion. What C compiler are you using? Did you set the CC env. variable at all? Please upload the following file (in its entirety) to a public website where I can download it $NWCHEM_TOP/src/tools/build/config.log
yurivict
commented
6 years ago @yurivict could you please stop pestering me with the story of the external GA library? I would like to get you a working environment for compiling NWChem and the tools compilation is extremely useful to iron out any problem. As I have ALREADY TOLD you several times, will try to provide a way to do to support external GA libraries but this is pretty low on my priorities.
Inflammatory rhetoric ignored.
What C compiler are you using? Did you set the CC env. variable at all?
CC=cc CXX=c++ (clang-5.0)
Please upload the following file (in its entirety) to a public website where I can download it $NWCHEM_TOP/src/tools/build/config.log
edoapra
commented
6 years ago Config.log shows that something is not quite right in your environment.
This is the part of config.log that puzzles me
configure:4851: checking whether the C compiler works
configure:4873: cc -fPIC -I. -I/usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/in\
clude -I/usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/install/include -DEX\
T_INT -DLINUX -DLINUX64 -DPARALLEL_DIAG -L/usr/ports/science/nwchem/work/nwchem-6.8.1/s\
rc/../lib/LINUX64 -L/usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/install/\
conftest.c -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lg\
radients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lpro\
perty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -l\
cafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -\
ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -ldimqm -lnwcutil -lga -larmci -lpeigs -lper\
fm -lcons -lbq -lnwcutil -lnwclapack -lnwcblas -L/usr/local/lib/gcc6 -L/usr/local/l\
ib/gcc6 -L/usr/local/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc6 -lpthread -lexec\
info -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -B/usr/local/bin -Wl,-rpath=/us\
r/local/lib/gcc6 -L/usr/local/lib/gcc6 -I/usr/local/include -I/usr/local/include -L/usr/l\
ocal/lib -lmpichf90 -Wl,-rpath -Wl,/usr/local/lib -lmpich -lopa -lmpl -lpthread -L/usr/lo\
cal/lib -lpthread >&5Why is the tools configure picking up stuff from config/makefile.h (libraries, headers, etc...)? This does not happen in my FreeBSD build and I can see this happening only if have env. variables (say CFLAGS or LDGLAGS) pointing to stuff from $NWCHEM_TOP/src/config/makefile.h
edoapra
commented
6 years ago Did you set F77=gfortran6 or FC=gfortran6? My advice is not to set either F77 or FC
yurivict
commented
6 years ago Here's the environment during build:
BSD_INSTALL_MAN=install -m 444
BSD_INSTALL_DATA=install -m 0644
BSD_INSTALL_SCRIPT=install -m 555
BSD_INSTALL_LIB=install -s -m 0644
BSD_INSTALL_PROGRAM=install -s -m 555
MANPREFIX=/usr/local
CXXFLAGS=-O2 -pipe -fno-omit-frame-pointer -fstack-protector -fno-strict-aliasing -fno-omit-frame-pointer
CXX=c++
LIBS=
LDFLAGS= -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -B/usr/local/bin -fstack-protector
CPPFLAGS=-fno-omit-frame-pointer
CPP=cpp
CFLAGS=-O2 -pipe -fno-omit-frame-pointer -fstack-protector -fno-strict-aliasing
CC=cc
LIBDIR=/usr/lib
LOCALBASE=/usr/local
PREFIX=/usr/local
STRINGS=/usr/local/bin/strings
SIZE=/usr/local/bin/size
READELF=/usr/local/bin/readelf
RANLIB=/usr/local/bin/ranlib
OBJDUMP=/usr/local/bin/objdump
OBJCOPY=/usr/local/bin/objcopy
NM=/usr/local/bin/nm
LD=/usr/local/bin/ld
GPROF=/usr/local/bin/gprof
CPPFILT=/usr/local/bin/c++filt
AS=/usr/local/bin/as
AR=/usr/local/bin/ar
ADDR2LINE=/usr/local/bin/addr2line
NO_LINT=YES
MK_KERNEL_SYMBOLS=no
MK_DEBUG_FILES=no
NO_PIE=yes
PATH=/usr/ports/science/nwchem/work/.bin:.:/home/yuri/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin
HOME=/usr/ports/science/nwchem/work
XDG_CONFIG_HOME=/usr/ports/science/nwchem/work
XDG_DATA_HOME=/usr/ports/science/nwchem/work
FCFLAGS=-Wl,-rpath=/usr/local/lib/gcc6
FFLAGS=-O -Wl,-rpath=/usr/local/lib/gcc6
FC=gfortran6
F77=gfortran6
USE_INTERNALBLAS=Y
USE_MPI=Y
NWCHEM_TARGET=LINUX64
NWCHEM_LONG_PATHS=Y
NWCHEM_MODULES=all
NWCHEM_TOP=/usr/ports/science/nwchem/work/nwchem-6.8.1/src/..
GTK_IM_MODULE=ibus
ARCH=amd64
OPSYS=FreeBSD
LOGNAME=yuri
LC_CTYPE=en_US.UTF-8
LANG=C
GLADE_PIXMAP_PATH=:
GLADE_MODULE_PATH=:
MAKELEVEL=1
XDG_DATA_DIRS=/usr/local/share:/usr/share
DESKTOP_SESSION=xfce
XDG_MENU_PREFIX=xfce-
XFCE4_SESSION_WITH_CK=1
XAUTHORITY=/home/yuri/.Xauthority
CLICOLOR=1
MAIL=/var/mail/yuri
META_MODE=normal
MAKEFLAGS= .MAKE.LEVEL.ENV=MAKELEVEL ARCH=amd64 HAVE_COMPAT_IA32_KERN=YES\ OPSYS=FreeBSD OSREL=11.1 OSVERSION=1101511 _OSRELEASE=11.1-STABLE _PERL5_FROM_BIN=5.24.3 _PKG_CHECKED=1 _SMP_CPUS=8
XDG_RUNTIME_DIR=/var/run/user/1001
_PERL5_FROM_BIN=5.24.3
SVN_EDITOR=vim
SESSION_MANAGER=local/yv.noip.me:/tmp/.ICE-unix/4153
OSREL=11.1
OLDPWD=/usr/ports/science/nwchem
SSH_AUTH_SOCK=/tmp/ssh-00hq4QH3OPOb/agent.4141
DISPLAY=unix:0.0
.MAKE.LEVEL.ENV=MAKELEVEL
_OSRELEASE=11.1-STABLE
PWD=/usr/ports/science/nwchem/work/nwchem-6.8.1/src
_SMP_CPUS=8
_=/usr/bin/make
XDG_CURRENT_DESKTOP=XFCE
HAVE_COMPAT_IA32_KERN=YES
VTE_VERSION=4803
TERM=xterm-256color
DBUS_SESSION_BUS_ADDRESS=unix:path=/tmp/dbus-V7zNukYYEO,guid=9960d04b738e3c6760dfd2705ab6f3d5
XMODIFIERS=@im=ibus
USER=yuri
CVSROOT=/usr/home/cvs
GLADE_CATALOG_PATH=:
SHELL=/bin/sh
COLORTERM=truecolor
_PKG_CHECKED=1
WINDOWID=33554435
LC_ALL=C
XDG_SESSION_COOKIE=yv.noip.me-1521939413.190040-381883269
XDG_CONFIG_DIRS=/etc/xdg:/usr/local/etc/xdg
SSH_AGENT_PID=4142
OSVERSION=1101511
SHLVL=1
QT_IM_MODULE=ibusI don't have nwchem pre-installed.
F77/FC is set to gfortran6 by the port building framework.
edoapra
commented
6 years ago I went back the config.log you provided and it clearly shows that both CPPFLAGS, LDFLAGS and LIBS are set to point to the, for now incomplete, NWChem installation. This is the cause of the compilation crash. I have no idea how this can be happening, do you?
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value=' -L/usr/ports/science/nwchem/work/nwchem-6.8.1/src/../lib/LINUX64 -L/usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/install/ '
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value='-I. -I/usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/i\
nclude -I/usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DPARALLEL_DIAG '
ac_cv_env_LIBS_set=set
ac_cv_env_LIBS_value='-lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf\
-lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -ldimqm -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -lnwclapack -lnwcblas -L/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -L/usr/local/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc6 -lpthread -lexecinfo -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -B/usr/local/bin -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -I/usr/local/include -I/usr/local/include -L/usr/local/lib -lmpichf90 -Wl,-rpath -Wl,/usr/local/lib -lmpich -lopa -lmpl -lpthread -L/usr/local/lib -lpthread 'If you are talking about this line and similar:
LDFLAGS=' -L/usr/ports/science/nwchem/work/nwchem-6.8.1/src/../lib/LINUX64 -L/usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/install/ 'this is set and printed internally by the build.
These values aren't in CPPFLAGS, LDFLAGS externally supplied in the environment, see the environment dump in my message above.
edoapra
commented
6 years ago How do I reproduce your environment? Please send instructions Thanks
edoapra
commented
6 years ago I have pushed a fix for better handling of gfortran-6 https://github.com/nwchemgit/nwchem/commit/05cf7e5c7ed5815d91a3785e8f8badad9a93ffdb This is not likely to fix your puzzling behavior CPPFLAGS, LDFLAGS and LIBS
yurivict
commented
6 years ago Instructions to reproduce the environment:
This will start the build and fail as it fails for me.
"make clean" will clean the build.
GH_TAGNAME=e36daf2 in the Makefile is the revision number. If you commit changes, just change it there and run "make makesum" to download the new tarball.
I will be happy to answer any additional questions.
jeffhammond
commented
6 years ago I have a FreeBSD 11.1 amd64 virtual machine running and have made reasonable progress on building NWChem therewithin. The biggest issue is that gcc is missing, or rather named gcc6. I'm having the compiler names in the build system for now. While I was able to create a binary, there was an issue with the GCC shared library versioning that prevents proper execution. This is a defect in the FreeBSD GCC toolchain that I will debug next week.
edoapra
commented
6 years ago Jeff
I have checked in fixes for gcc-6 and gfortran-6.
https://github.com/nwchemgit/nwchem/commit/6685039aad6b078a59c24e297bcbe8ae4bec33d4
Is your compiler named gcc-6 or gcc6?
On 3/26/18 5:10 PM, Jeff Hammond wrote:
I have a FreeBSD 11.1 amd64 virtual machine running and have made reasonable progress on building NWChem therewithin. The biggest issue is that gcc is missing, or rather named gcc6. I'm having the compiler names in the build system for now. While I was able to create a binary, there was an issue with the GCC shared library versioning that prevents proper execution. This is a defect in the FreeBSD GCC toolchain that I will debug next week.
— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/nwchemgit/nwchem/issues/30#issuecomment-376352482, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AE8hoeK2GXBfwLaihj1ekZIWWrnk5bF0ks5tiYN0gaJpZM4S7kFP.
yurivict
commented
6 years ago While I was able to create a binary, there was an issue with the GCC shared library versioning that prevents proper execution. This is a defect in the FreeBSD GCC toolchain that I will debug next week.
What's the gcc versioning defect?
edoapra
commented
6 years ago Checked in a fix for gcc6 and gfortran6
https://github.com/nwchemgit/nwchem/commit/9f1071033776c80f4c16f05252c30e2dc0a64016
On 3/26/18 5:12 PM, Edoardo Apra wrote:
Jeff
I have checked in fixes for gcc-6 and gfortran-6.
https://github.com/nwchemgit/nwchem/commit/6685039aad6b078a59c24e297bcbe8ae4bec33d4
Is your compiler named gcc-6 or gcc6?
On 3/26/18 5:10 PM, Jeff Hammond wrote:
I have a FreeBSD 11.1 amd64 virtual machine running and have made reasonable progress on building NWChem therewithin. The biggest issue is that gcc is missing, or rather named gcc6. I'm having the compiler names in the build system for now. While I was able to create a binary, there was an issue with the GCC shared library versioning that prevents proper execution. This is a defect in the FreeBSD GCC toolchain that I will debug next week.
— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/nwchemgit/nwchem/issues/30#issuecomment-376352482, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AE8hoeK2GXBfwLaihj1ekZIWWrnk5bF0ks5tiYN0gaJpZM4S7kFP.
edoapra
commented
6 years ago Jeff
Since I am using a VM myself, I wonder if you stumbled into the same error that, in my case, was caused by hostname not being defined.
My error message was more or less this one below
[mpiexec at node-0-25.local control_cb (pm/pmiserv/pmiserv_cb.c:200): assert (!closed) failed [mpiexec at node-0-25.localHYDT_dmxu_poll_wait_for_event (tools/demux/demux_poll.c:76): callback returned error status [mpiexec at node-0-25.localHYD_pmci_wait_for_completion (pm/pmiserv/pmiserv_pmci.c:198): error waiting for event [mpiexec at node-0-25.local main (ui/mpich/mpiexec.c:344): process manager error waiting for completion
On 3/26/18 5:10 PM, Jeff Hammond wrote:
I have a FreeBSD 11.1 amd64 virtual machine running and have made reasonable progress on building NWChem therewithin. The biggest issue is that gcc is missing, or rather named gcc6. I'm having the compiler names in the build system for now. While I was able to create a binary, there was an issue with the GCC shared library versioning that prevents proper execution. This is a defect in the FreeBSD GCC toolchain that I will debug next week.
— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/nwchemgit/nwchem/issues/30#issuecomment-376352482, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AE8hoeK2GXBfwLaihj1ekZIWWrnk5bF0ks5tiYN0gaJpZM4S7kFP.
edoapra
commented
6 years ago Latest commit https://github.com/nwchemgit/nwchem/commit/e0513353586274242b45e00846c05a4f2264f62f brings the tools directory compilation to completion under the ports environment
GH_TAGNAME= e051335 Revision e051335 breaks in shell scripts:
===> Building for nwchem-6.8.1
gmake[1]: Entering directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src'
[: -gt: unexpected operator
[: -gt: unexpected operator
gmake -C config -f make_nwchem_config NWCHEM_MODULES="all"
gmake[2]: Entering directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src/config'Edo:
My issue was something like “libgcc_s.so ... GCC_4.6.0 ... libgfortran.so” for serial job launched without mpirun/mpiexec (I can’t remote into the VM to quote exact issue). This may be caused by switching MPICH packages or something similar. I’ll just build GCC and/or MPICH from source next time I try to build. Then I’ll try LLVM (flang+clang). Won’t be until next week though.
edoapra
commented
6 years ago @yurivict Please provide
edoapra
commented
6 years ago @jeffhammond Your error message looks odd to me: why is gfortran-6 using libraries from gcc 4.6.0 ... did you give up on gfortran-6 and switch to an older gcc version?
jeffhammond
commented
6 years ago Yeah, it’s weird. I think I screwed up build by uninstalling scalapack after GA configure but before NWChem build. I never installed GCC4 but probably the scalapack package binary used it.
edoapra
commented
6 years ago @yurivict I might have fixed your latest problem. Please use the latest hotfix/release-6-8 tree https://github.com/nwchemgit/nwchem/commit/b3b9bb3e511e001cf647dfa3ca84b7c521be6ffc GH_TAGNAME=b3b9bb3
edoapra
commented
6 years ago @jeffhammond Jeff, the following might fix your linking issue
edoapra
commented
6 years ago The following GA patch might be needed to support 32-bit linear algebra in FreeBSD https://github.com/GlobalArrays/ga/pull/101
yurivict
commented
6 years ago You closed this, but do you have instructions how to build it on FreeBSD?
It fails with GH_TAGNAME=b3b9bb3.
There are numerous errors like this:
grep: /usr/ports/science/nwchem/work/nwchem-6.8.1/src/../src/tools/build/Makefile: No such file or directoryand similar failures of commands run from gmake.
It fails in the end:
checking for gfortran6 flush routine... flush
checking for flag to disable gfortran6 main when linking with C main... none
checking for routines to access the command line from Fortran... yes
checking whether Fortran hidden string length convention is after args...
configure: error: f2c string convention is neither after args nor after string
gmake[2]: *** [GNUmakefile:669: build/config.status] Error 1
gmake[2]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src/tools'
gmake[1]: *** [GNUmakefile:103: libraries] Error 1
gmake[1]: Leaving directory '/usr/ports/science/nwchem/work/nwchem-6.8.1/src'Please provide a more detailed bug report by uploading
I couldn't make it run on FreeBSD. FreeBSD is much like linux. GA port exists, so there's no need to download it.
I tried to create the FreeBSD port for it, but couldn't do this by myself. I am happy to answer any questions related to FreeBSD itself.
Originally reported here: https://github.com/nwchemgit/nwchem/issues/29