search

Electrostatics / apbs

Software for biomolecular electrostatics and solvation calculations
http://www.poissonboltzmann.org/
Other
94 stars 26 forks source link

cmake error , please help me #243

Closed Shingzzz closed 1 year ago

Shingzzz commented 2 years ago

Describe the bug hello guys, I would like to install apbs 3.4.1 from source code , but I met a lot of errors , I try to solve a little of them , such as dependencies and environmental path . There is a error that I think I can`t solve.

CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
  Could NOT find Python3: Found unsuitable version "3.7.9", but required is
  exact version "3.6" (found /usr/bin/python3)

do I have to use python3.6 ? I can`t change the python version casually .

To Reproduce Steps to reproduce the behavior:

git clone apbs
cd apbs

vim CMakeLists.txt
#I change the no.116 ON->OFF
option(APBS_STATIC_BUILD "Flag to indicate whether a static build should be used (if false, will be dynamic)" OFF)

mkdir build
cd build

export APBS_BUILD_DIR=`echo $(pwd)`
export INSTALL_DIR=/usr/local/apbs
export PATH=$INSTALL_DIR/bin:$PATH
cmake -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR 
-DENABLE_GEOFLOW=ON 
-DENABLE_BEM=ON 
-DENABLE_OPENMP=ON 
-DENABLE_PYTHON=ON 
-DENABLE_TESTS=ON 
-DBUILD_SHARED_LIBS=ON 
-DENABLE_PBAM=OFF 
-DENABLE_PBSAM=OFF 
-DCMAKE_C_COMPILER=/root/install_path/bisheng-compiler-2.1.0/bin/clang 
-DCMAKE_CXX_COMPILER=/root/install_path/bisheng-compiler-2.1.0/bin/clang++ 
..

Context

-- The C compiler identification is Clang 12.0.0
-- The CXX compiler identification is Clang 12.0.0
-- Check for working C compiler: /root/install_path/bisheng-compiler-2.1.0/bin/clang
-- Check for working C compiler: /root/install_path/bisheng-compiler-2.1.0/bin/clang -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /root/install_path/bisheng-compiler-2.1.0/bin/clang++
-- Check for working CXX compiler: /root/install_path/bisheng-compiler-2.1.0/bin/clang++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Install prefix: /usr/local/apbs
-- 
-- APBS Static build: OFF
-- Building shared libs: ON
-- Find-library suffixes: .so;.so;.a
-- 
-- Building FETK from commit 57195e55351e04ce6ee0ef56a143c996a9aee7e2
-- FETK set_basic_vars_and_paths: FALSE, FETK
-- Setting project paths
-- Install prefix: /usr/local/apbs
-- FETK static build: OFF
-- Building shared libs: ON
-- Find-library suffixes: .so;.so;.so;.a
Configuring build for MALOC
-- FETK set_basic_vars_and_paths: FALSE, maloc
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of mode_t
-- Check size of mode_t - done
-- Check size of pid_t
-- Check size of pid_t - done
-- Check size of size_t
-- Check size of size_t - done
-- Looking for 4 include files stdlib.h, ..., float.h
-- Looking for 4 include files stdlib.h, ..., float.h - found
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file sys/socket.h
-- Looking for include file sys/socket.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file sys/un.h
-- Looking for include file sys/un.h - found
-- Looking for include file sys/wait.h
-- Looking for include file sys/wait.h - found
-- Looking for include file netinet/in.h
-- Looking for include file netinet/in.h - found
-- Looking for include file arpa/inet.h
-- Looking for include file arpa/inet.h - found
-- Looking for include file netdb.h
-- Looking for include file netdb.h - found
-- Looking for include file sys/stat.h
-- Looking for include file sys/stat.h - found
-- Looking for include file fcntl.h
-- Looking for include file fcntl.h - found
-- Looking for include file rpc/rpc.h
-- Looking for include file rpc/rpc.h - not found
CMake Warning at build/_deps/fetk-src/cmake/FETKBuildFunctions.cmake:230 (message):
  Missing/invalid rpc/rpc.h header.  XDR support disabled
Call Stack (most recent call first):
  build/_deps/fetk-src/maloc/CMakeLists.txt:49 (header_and_type_checks)

-- Looking for getcwd
-- Looking for getcwd - found
-- Looking for O_NONBLOCK
-- Looking for O_NONBLOCK - found
-- Type: INTERNAL_HEADERS
-- Items: /root/apbs/build/_deps/fetk-build/maloc/src/maloccf.h
-- Type: SOURCES
-- Items: maloc_base.c
-- Type: EXTERNAL_HEADERS
-- Items: maloc/maloc.h;maloc/maloc_base.h
-- Type: INTERNAL_HEADERS
-- Items: maloc_base_p.h
-- Type: SOURCES
-- Items: psh.c;vcom.c;vmp.c;vmpi.c
-- Type: EXTERNAL_HEADERS
-- Items: maloc/psh.h;maloc/vcom.h;maloc/vmp.h;maloc/vmpi.h
-- Type: INTERNAL_HEADERS
-- Items: psh_p.h;vcom_p.h;vmpi_p.h;vmp_p.h
-- Type: SOURCES
-- Items: vlex.c;vpars.c;vpup.c;vsh.c;vyacc.c
-- Type: EXTERNAL_HEADERS
-- Items: maloc/vsh.h
-- Type: INTERNAL_HEADERS
-- Items: vpup.h;vsh_p.h;vyacc.h
-- Type: SOURCES
-- Items: vio.c;viofb.c;vmem.c;vnm.c;vnmfb.c;vpred.c;vset.c;ziofb.c
-- Type: EXTERNAL_HEADERS
-- Items: maloc/vio.h;maloc/vmem.h;maloc/vnm.h;maloc/vset.h;maloc/vsys.h;maloc/vpred.h
-- Type: INTERNAL_HEADERS
-- Items: vio_p.h;vmem_p.h;vnm_p.h;vpred_p.h;vset_p.h
Configuring build for PUNC
-- FETK set_basic_vars_and_paths: FALSE, punc
CMake Warning at build/_deps/fetk-src/cmake/FETKBuildFunctions.cmake:230 (message):
  Missing/invalid rpc/rpc.h header.  XDR support disabled
Call Stack (most recent call first):
  build/_deps/fetk-src/punc/CMakeLists.txt:26 (header_and_type_checks)

-- Will build vf2c
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib64/libopenblas.a  
-- Could NOT find SuperLU (missing: SUPERLU_INCLUDES SUPERLU_LIBRARIES SUPERLU_VERSION_OK) 
-- Will build SuperLU
-- Will build ARPACK
-- Will build CGCODE
-- Building vf2c
-- Type: EXTERNAL_HEADERS
-- Items: punc/varpack.h;punc/vblas.h;punc/vcgcode.h;punc/vlapack.h;punc/vpmg.h;punc/vf2c.h
-- Type: INTERNAL_HEADERS
-- Items: f2c.h;fio.h;fmt.h;fp.h;lio.h;rawio.h;signal1.h;sysdep1.h
-- Type: SOURCES
-- Items: f77vers.c;i77vers.c;s_rnge.c;abort_.c;exit_.c;getarg_.c;iargc_.c;getenv_.c;signal_.c;s_stop.c;s_paus.c;system_.c;cabs.c;derf_.c;derfc_.c;erf_.c;erfc_.c;sig_die.c;uninit.c;pow_ci.c;pow_dd.c;pow_di.c;pow_hh.c;pow_ii.c;pow_ri.c;pow_zi.c;pow_zz.c;c_abs.c;c_cos.c;c_div.c;c_exp.c;c_log.c;c_sin.c;c_sqrt.c;z_abs.c;z_cos.c;z_div.c;z_exp.c;z_log.c;z_sin.c;z_sqrt.c;r_abs.c;r_acos.c;r_asin.c;r_atan.c;r_atn2.c;r_cnjg.c;r_cos.c;r_cosh.c;r_dim.c;r_exp.c;r_imag.c;r_int.c;r_lg10.c;r_log.c;r_mod.c;r_nint.c;r_sign.c;r_sin.c;r_sinh.c;r_sqrt.c;r_tan.c;r_tanh.c;d_abs.c;d_acos.c;d_asin.c;d_atan.c;d_atn2.c;d_cnjg.c;d_cos.c;d_cosh.c;d_dim.c;d_exp.c;d_imag.c;d_int.c;d_lg10.c;d_log.c;d_mod.c;d_nint.c;d_prod.c;d_sign.c;d_sin.c;d_sinh.c;d_sqrt.c;d_tan.c;d_tanh.c;i_abs.c;i_dim.c;i_dnnt.c;i_indx.c;i_len.c;i_mod.c;i_nint.c;i_sign.c;lbitbits.c;lbitshft.c;h_abs.c;h_dim.c;h_dnnt.c;h_indx.c;h_len.c;h_mod.c;h_nint.c;h_sign.c;l_ge.c;l_gt.c;l_le.c;l_lt.c;hl_ge.c;hl_gt.c;hl_le.c;hl_lt.c;ef1asc_.c;ef1cmc_.c;f77_aloc.c;s_cat.c;s_cmp.c;s_copy.c;dtime_.c;etime_.c;backspac.c;close.c;dfe.c;dolio.c;due.c;endfile.c;err.c;fmt.c;fmtlib.c;ftell_.c;iio.c;ilnw.c;inquire.c;lread.c;lwrite.c;open.c;rdfmt.c;rewind.c;rsfe.c;rsli.c;rsne.c;sfe.c;sue.c;typesize.c;uio.c;util.c;wref.c;wrtfmt.c;wsfe.c;wsle.c;wsne.c;xwsne.c;main.c
-- Building cgcode
-- Type: INTERNAL_HEADERS
-- Items: vcgcode.h
-- Type: SOURCES
-- Items: scgdrv.c;scg.c;scr.c;scrind.c;spcg.c;scgnr.c;scgne.c;spcgnr.c;spcgne.c;sppcg.c;spcgca.c;sdpchb.c;scbfix.c;sckchb.c;scgchk.c;sonest.c;msstop.c;r1mach.c;sratqr.c;dcgdrv.c;dcg.c;dcr.c;dcrind.c;dpcg.c;dcgnr.c;dcgne.c;dpcgnr.c;dpcgne.c;dppcg.c;dpcgca.c;ddpchb.c;dcbfix.c;dckchb.c;dcgchk.c;donest.c;mdstop.c;d1mach.c;dratqr.c;depsln.c
-- Building arpack
-- Type: INTERNAL_HEADERS
-- Items: varpack.h
-- Type: SOURCES
-- Items: sgetv0.c;slaqrb.c;sstqrb.c;ssortc.c;ssortr.c;sstatn.c;sstats.c;snaitr.c;snapps.c;snaup2.c;snaupd.c;snconv.c;sneigh.c;sngets.c;ssaitr.c;ssapps.c;ssaup2.c;ssaupd.c;ssconv.c;sseigt.c;ssgets.c;sneupd.c;sseupd.c;ssesrt.c;dgetv0.c;dlaqrb.c;dstqrb.c;dsortc.c;dsortr.c;dstatn.c;dstats.c;dnaitr.c;dnapps.c;dnaup2.c;dnaupd.c;dnconv.c;dneigh.c;dngets.c;dsaitr.c;dsapps.c;dsaup2.c;dsaupd.c;dsconv.c;dseigt.c;dsgets.c;dneupd.c;dseupd.c;dsesrt.c;cnaitr.c;cnapps.c;cnaup2.c;cnaupd.c;cneigh.c;cneupd.c;cngets.c;cgetv0.c;csortc.c;cstatn.c;znaitr.c;znapps.c;znaup2.c;znaupd.c;zneigh.c;zneupd.c;zngets.c;zgetv0.c;zsortc.c;zstatn.c;cmout.c;cvout.c;dmout.c;dvout.c;icnteq.c;icopy.c;iset.c;iswap.c;ivout.c;second.c;smout.c;svout.c;zmout.c;zvout.c
CMake Warning (dev) at build/_deps/superlu-src/CMakeLists.txt:11 (project):
  Policy CMP0048 is not set: project() command manages VERSION variables.
  Run "cmake --help-policy CMP0048" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The following variable(s) would be set to empty:

    PROJECT_VERSION
    PROJECT_VERSION_MAJOR
    PROJECT_VERSION_MINOR
    PROJECT_VERSION_PATCH
This warning is for project developers.  Use -Wno-dev to suppress it.

Process XSDK defaults ...
USE_XSDK_DEFAULTS = 'FALSE'
-- SuperLU will be built as a shared library.
-- Using TPL_BLAS_LIBRARIES=''
-- Type: INTERNAL_HEADERS
-- Items: /root/apbs/build/_deps/fetk-build/punc/src/punccf.h
-- Type: SOURCES
-- Items: punc_base.c
-- Type: EXTERNAL_HEADERS
-- Items: punc/punc.h;punc/punc_base.h
-- Type: INTERNAL_HEADERS
-- Items: punc_base_p.h
Configuring build for GAMER
-- FETK set_basic_vars_and_paths: FALSE, gamer
CMake Warning at build/_deps/fetk-src/cmake/FETKBuildFunctions.cmake:230 (message):
  Missing/invalid rpc/rpc.h header.  XDR support disabled
Call Stack (most recent call first):
  build/_deps/fetk-src/gamer/CMakeLists.txt:25 (header_and_type_checks)

-- Type: INTERNAL_HEADERS
-- Items: /root/apbs/build/_deps/fetk-build/gamer/src/gamercf.h
-- Type: SOURCES
-- Items: gamer_base.c
-- Type: EXTERNAL_HEADERS
-- Items: gamer/gamer.h;gamer/gamer_base.h
-- Type: INTERNAL_HEADERS
-- Items: gamer_base_p.h
-- Type: SOURCES
-- Items: triangle.c
-- Type: EXTERNAL_HEADERS
-- Items: gamer/triangle.h
-- Type: INTERNAL_HEADERS
-- Items: triangle_p.h
-- Type: SOURCES
-- Items: predicates.cpp;tetgen.cpp
-- Type: EXTERNAL_HEADERS
-- Items: gamer/tetgen.h
-- Type: INTERNAL_HEADERS
-- Items: tetgen_p.h
-- Type: SOURCES
-- Items: CorrectNormals.C;GenerateSphereMesh.C;MarchingCube.C;PDB2Mesh.C;PDB2Volume.C;ReadLattice.C;ReadPDB.C;ReadWriteMesh.C;RegionGrowing.C;SurfaceMesh.C;SurfExtract.C;SurfRefine.C;SurfSmooth.C
-- Type: EXTERNAL_HEADERS
-- Items: gamer/biom.h
-- Type: INTERNAL_HEADERS
-- Items: MarchingCube.h;PDB2Volume.h
Configuring build for MC
-- FETK set_basic_vars_and_paths: FALSE, mc
CMake Warning at build/_deps/fetk-src/cmake/FETKBuildFunctions.cmake:230 (message):
  Missing/invalid rpc/rpc.h header.  XDR support disabled
Call Stack (most recent call first):
  build/_deps/fetk-src/mc/CMakeLists.txt:25 (header_and_type_checks)

-- Found UMFPACK: /usr/include/suitesparse  
-- @@@@ finding blas
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- @@@@ finding lapack
-- %%%%% list of libraries: 
-- Testing libraries: TRUE
--     CMAKE_REQUIRED_LIBRARIES: /usr/lib64/libopenblas.a;-lpthread;-lm;-ldl
-- checking for function cheev_
--     result: TRUE
-- Found LAPACK: /usr/lib64/libopenblas.a;-lpthread;-lm;-ldl  
-- @@@@ finding amd
-- Found AMD headers in: /usr/include/suitesparse
-- Found AMD library: /usr/lib64/libamd.so
-- @@@@ finding camd
-- Found CAMD headers in: /usr/include/suitesparse
-- Found CAMD library: /usr/lib64/libcamd.so
-- @@@@ finding colamd
-- Found COLAMD headers in: /usr/include/suitesparse
-- Found COLAMD library: /usr/lib64/libcolamd.so
-- @@@@ finding ccolamd
-- Found CCOLAMD headers in: /usr/include/suitesparse
-- Found CCOLAMD library: /usr/lib64/libccolamd.so
-- @@@@ finding cholmod
-- Found CHOLMOD headers in: /usr/include/suitesparse
-- Found CHOLMOD library: /usr/lib64/libcholmod.so
-- @@@@ finding parseqr
-- Found SUITESPARSEQR headers in: /usr/include/suitesparse
-- Found SUITESPARSEQR library: /usr/lib64/libspqr.so
-- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB.
-- @@@@ finding config
-- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse
-- Found SUITESPARSE_CONFIG library: /usr/lib64/libsuitesparseconfig.so
-- Found LIBRT library: /usr/lib64/librt.so
-- Adding librt: /usr/lib64/librt.so to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing).
-- @@@@ finding metis
-- Did not find METIS library (optional SuiteSparse dependency)
-- Found SuiteSparse: TRUE (found version "4.4.6") 
-- Type: INTERNAL_HEADERS
-- Items: /root/apbs/build/_deps/fetk-build/mc/src/mccf.h
-- Type: SOURCES
-- Items: mc_base.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/mc_base.h;mc/mc.h
-- Type: INTERNAL_HEADERS
-- Items: mc_base_p.h
-- Type: SOURCES
-- Items: bmat.c;bsolv.c;bvec.c;mat.c;matcopy.c;matln.c;mtool.c;slu.c;vec.c;vec3.c;zslu.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/bam.h;mc/bmat.h;mc/bvec.h;mc/mat.h;mc/mtool.h;mc/slu.h;mc/vec.h;mc/vec3.h;mc/zslu.h
-- Type: INTERNAL_HEADERS
-- Items: bam_p.h;bmat_p.h;bvec_p.h;mat_p.h;mtool_p.h;slu_p.h;vec_p.h;vec3_p.h;zslu_p.h
-- Type: SOURCES
-- Items: whb.c;bvechb.c;hbtools.c;rcmat.c;brcmat.c;subopt.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/whb.h
-- Type: INTERNAL_HEADERS
-- Items: brcmat_p.h;bvechb_p.h;cholesky_p.h;hbtools_p.h;rcmat_p.h;subopt_p.h;whb_p.h
-- Type: SOURCES
-- Items: aprx.c;assem.c;bnode.c;estim.c;eval.c;io.c;node.c;parti.c;re.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/aprx.h;mc/bnode.h;mc/node.h;mc/re.h
-- Type: INTERNAL_HEADERS
-- Items: aprx_p.h;bnode_p.h;node_p.h;re_p.h
-- Type: SOURCES
-- Items: vel.c;ves.c;gem.c;gemchk.c;gemdisp.c;gemg.c;gemgen.c;gemio.c;gemref.c;gemunref.c;gemcube.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/gem.h;mc/vel.h;mc/ves.h
-- Type: INTERNAL_HEADERS
-- Items: gem_p.h;vel_p.h;ves_p.h
-- Type: SOURCES
-- Items: pde.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/pde.h
-- Type: INTERNAL_HEADERS
-- Items: pde_p.h
-- Type: SOURCES
-- Items: am.c;lsolv.c;nsolv.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/am.h;mc/nam.h
-- Type: INTERNAL_HEADERS
-- Items: am_p.h;nam_p.h
-- Type: SOURCES
-- Items: dyn.c;svio.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/dyn.h
-- Type: INTERNAL_HEADERS
-- Items: dyn_p.h;svio_p.h
-- Type: SOURCES
-- Items: mcsh.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/mcsh.h
-- Type: INTERNAL_HEADERS
-- Items: mcsh_p.h
-- #############################################################
-- ** PROJECT NAME:  APBS
-- ** PROJECT DESC:  Adaptive Poisson-Boltzmann Solver
-- ** PROJECT URL:   http://www.poissonboltzmann.org/
-- ** VERSION_DATA:  3.4.1
-- ** CURRENT_TIME:  2022-09-14T16:00:42
-- ** CURRENT_YEAR:  2022
-- Setting project paths
-- Setting lookup paths for headers and libraries
-- Computing machine epsilon values
-- Floating point epsilon is 2.220446e-16
-- Double precision epsilon is 2.220446e-16
-- Looking for time
-- Looking for time - found
-- Looking for rand
-- Looking for rand - found
-- Looking for srand
-- Looking for srand - found
-- Found Intl: /usr/include  
-- Performing Test Iconv_IS_BUILT_IN
-- Performing Test Iconv_IS_BUILT_IN - Success
-- Found Iconv: /usr/lib64/libc.so  
-- @@@@ finding blas
-- @@@@ finding lapack
-- %%%%% list of libraries: 
-- Testing libraries: TRUE
--     CMAKE_REQUIRED_LIBRARIES: /usr/lib64/libopenblas.a;-lpthread;-lm;-ldl
-- checking for function cheev_
--     result: TRUE
-- @@@@ finding amd
-- Found AMD headers in: /usr/include/suitesparse
-- Found AMD library: /usr/lib64/libamd.so
-- @@@@ finding camd
-- Found CAMD headers in: /usr/include/suitesparse
-- Found CAMD library: /usr/lib64/libcamd.so
-- @@@@ finding colamd
-- Found COLAMD headers in: /usr/include/suitesparse
-- Found COLAMD library: /usr/lib64/libcolamd.so
-- @@@@ finding ccolamd
-- Found CCOLAMD headers in: /usr/include/suitesparse
-- Found CCOLAMD library: /usr/lib64/libccolamd.so
-- @@@@ finding cholmod
-- Found CHOLMOD headers in: /usr/include/suitesparse
-- Found CHOLMOD library: /usr/lib64/libcholmod.so
-- @@@@ finding parseqr
-- Found SUITESPARSEQR headers in: /usr/include/suitesparse
-- Found SUITESPARSEQR library: /usr/lib64/libspqr.so
-- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB.
-- @@@@ finding config
-- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse
-- Found SUITESPARSE_CONFIG library: /usr/lib64/libsuitesparseconfig.so
-- Found LIBRT library: /usr/lib64/librt.so
-- Adding librt: /usr/lib64/librt.so to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing).
-- @@@@ finding metis
-- Did not find METIS library (optional SuiteSparse dependency)
-- UMFPack libraries: /usr/lib64/libumfpack.so
-- SUITESPARSE_INCLUDE_DIRS: /usr/include/suitesparse
-- SUITESPARSE_LIBRARIES: /usr/lib64/libspqr.so;/usr/lib64/libcholmod.so;/usr/lib64/libccolamd.so;/usr/lib64/libcamd.so;/usr/lib64/libcolamd.so;/usr/lib64/libamd.so;/usr/lib64/libopenblas.a;-lpthread;-lm;-ldl;/usr/lib64/libopenblas.a;/usr/lib64/libsuitesparseconfig.so;/usr/lib64/librt.so
-- Building TABIPB
-- Found OpenMP_C: -fopenmp=libomp (found version "5.0") 
-- Found OpenMP_CXX: -fopenmp=libomp (found version "5.0") 
-- Found OpenMP: TRUE (found version "5.0")  
-- Copying NanoShaper executable
-- NanoShaper download: https://github.com/lwwilson1/mesh_routines/releases/download/v1.6/NanoShaper_Linux64 /root/apbs/build/_deps/tabi-build/bin/NanoShaper
-- Copying NanoShaper executable
-- NanoShaper Download: https://github.com/lwwilson1/mesh_routines/releases/download/v1.6/NanoShaper_Linux64 /root/apbs/build/temp/NanoShaper
-- Building GEOFLOW
-- Found Boost: /usr/include (found version "1.73.0")  
-- Found Python: /usr/bin/python3.7 (found version "3.7.9") found components: Interpreter 
-- Inline functions enabled
-- Verbose debugging mode enabled
-- Checking for OpenMP
-- Found OpenMP_C: -fopenmp=libomp  
-- Found OpenMP_CXX: -fopenmp=libomp  
-- Found OpenMP: TRUE   
-- OpenMP support enabled
-- Building of iAPBS interface disabled
-- Adding apbs_generic
-- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c
-- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h
-- With internal header files 
-- With library dependencies mc;util;dl;m;stdc++;/usr/lib64/libc.so;-lpthread;/usr/lib64/libumfpack.so;/usr/lib64/libspqr.so;/usr/lib64/libcholmod.so;/usr/lib64/libccolamd.so;/usr/lib64/libcamd.so;/usr/lib64/libcolamd.so;/usr/lib64/libamd.so;/usr/lib64/libopenblas.a;-lpthread;-lm;-ldl;/usr/lib64/libopenblas.a;/usr/lib64/libsuitesparseconfig.so;/usr/lib64/librt.so;TABIPBlib;GeometricFlowLib;-fopenmp=libomp
-- Added apbs_generic
-- Adding apbs_pmgc
-- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c
-- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h
-- With internal header files 
-- With library dependencies mc;util;dl;m;stdc++;/usr/lib64/libc.so;-lpthread;/usr/lib64/libumfpack.so;/usr/lib64/libspqr.so;/usr/lib64/libcholmod.so;/usr/lib64/libccolamd.so;/usr/lib64/libcamd.so;/usr/lib64/libcolamd.so;/usr/lib64/libamd.so;/usr/lib64/libopenblas.a;-lpthread;-lm;-ldl;/usr/lib64/libopenblas.a;/usr/lib64/libsuitesparseconfig.so;/usr/lib64/librt.so;TABIPBlib;GeometricFlowLib;-fopenmp=libomp
-- Added apbs_pmgc
-- Adding apbs_mg
-- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c
-- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h
-- With internal header files 
-- With library dependencies mc;util;dl;m;stdc++;/usr/lib64/libc.so;-lpthread;/usr/lib64/libumfpack.so;/usr/lib64/libspqr.so;/usr/lib64/libcholmod.so;/usr/lib64/libccolamd.so;/usr/lib64/libcamd.so;/usr/lib64/libcolamd.so;/usr/lib64/libamd.so;/usr/lib64/libopenblas.a;-lpthread;-lm;-ldl;/usr/lib64/libopenblas.a;/usr/lib64/libsuitesparseconfig.so;/usr/lib64/librt.so;TABIPBlib;GeometricFlowLib;-fopenmp=libomp;apbs_generic;apbs_pmgc
-- Added apbs_mg
-- Adding apbs_fem
-- With source files vcsm.c;vfetk.c;vpee.c
-- With external header files vcsm.h;vfetk.h;vpee.h
-- With internal header files 
-- With library dependencies mc;util;dl;m;stdc++;/usr/lib64/libc.so;-lpthread;/usr/lib64/libumfpack.so;/usr/lib64/libspqr.so;/usr/lib64/libcholmod.so;/usr/lib64/libccolamd.so;/usr/lib64/libcamd.so;/usr/lib64/libcolamd.so;/usr/lib64/libamd.so;/usr/lib64/libopenblas.a;-lpthread;-lm;-ldl;/usr/lib64/libopenblas.a;/usr/lib64/libsuitesparseconfig.so;/usr/lib64/librt.so;TABIPBlib;GeometricFlowLib;-fopenmp=libomp;apbs_generic
-- Added apbs_fem
-- Adding apbs_geoflow_apbs
-- With source files geoflow_wrap_apbs.cpp
-- With external header files geoflow_wrap_apbs.h
-- With internal header files 
-- With library dependencies mc;util;dl;m;stdc++;/usr/lib64/libc.so;-lpthread;/usr/lib64/libumfpack.so;/usr/lib64/libspqr.so;/usr/lib64/libcholmod.so;/usr/lib64/libccolamd.so;/usr/lib64/libcamd.so;/usr/lib64/libcolamd.so;/usr/lib64/libamd.so;/usr/lib64/libopenblas.a;-lpthread;-lm;-ldl;/usr/lib64/libopenblas.a;/usr/lib64/libsuitesparseconfig.so;/usr/lib64/librt.so;TABIPBlib;GeometricFlowLib;-fopenmp=libomp
-- Added apbs_geoflow_apbs
-- Adding apbs_routines
-- With source files routines.c
-- With external header files 
-- With internal header files 
-- With library dependencies mc;util;dl;m;stdc++;/usr/lib64/libc.so;-lpthread;/usr/lib64/libumfpack.so;/usr/lib64/libspqr.so;/usr/lib64/libcholmod.so;/usr/lib64/libccolamd.so;/usr/lib64/libcamd.so;/usr/lib64/libcolamd.so;/usr/lib64/libamd.so;/usr/lib64/libopenblas.a;-lpthread;-lm;-ldl;/usr/lib64/libopenblas.a;/usr/lib64/libsuitesparseconfig.so;/usr/lib64/librt.so;TABIPBlib;GeometricFlowLib;-fopenmp=libomp;mc;util;dl;m;stdc++;/usr/lib64/libc.so;-lpthread;/usr/lib64/libumfpack.so;/usr/lib64/libspqr.so;/usr/lib64/libcholmod.so;/usr/lib64/libccolamd.so;/usr/lib64/libcamd.so;/usr/lib64/libcolamd.so;/usr/lib64/libamd.so;/usr/lib64/libopenblas.a;-lpthread;-lm;-ldl;/usr/lib64/libopenblas.a;/usr/lib64/libsuitesparseconfig.so;/usr/lib64/librt.so;TABIPBlib;GeometricFlowLib;-fopenmp=libomp;apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_geoflow_apbs
-- Added apbs_routines
-- External Headers: 
--  
-- APBS Libraries: mc;util;dl;m;stdc++;/usr/lib64/libc.so;-lpthread;/usr/lib64/libumfpack.so;/usr/lib64/libspqr.so;/usr/lib64/libcholmod.so;/usr/lib64/libccolamd.so;/usr/lib64/libcamd.so;/usr/lib64/libcolamd.so;/usr/lib64/libamd.so;/usr/lib64/libopenblas.a;-lpthread;-lm;-ldl;/usr/lib64/libopenblas.a;/usr/lib64/libsuitesparseconfig.so;/usr/lib64/librt.so;TABIPBlib;GeometricFlowLib;-fopenmp=libomp
-- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_geoflow_apbs;apbs_routines
--  
-- -march=armv8.2-a  -fsigned-char -ffp-contract=off -fPIC
-- Building documentation enabled
-- ================================================================
-- ================================================================
-- Supplemental tools enabled
-- Building mesh
-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines
-- Building manip
-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines
-- Found SWIG: /usr/bin/swig (found version "3.0.12") 
CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
  Could NOT find Python3: Found unsuitable version "3.7.9", but required is
  exact version "3.6" (found /usr/bin/python3)
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:391 (_FPHSA_FAILURE_MESSAGE)
  /usr/share/cmake/Modules/FindPython/Support.cmake:2261 (find_package_handle_standard_args)
  /usr/share/cmake/Modules/FindPython3.cmake:300 (include)
  tools/python/CMakeLists.txt:12 (find_package)

-- Configuring incomplete, errors occurred!
See also "/root/apbs/build/CMakeFiles/CMakeOutput.log".
See also "/root/apbs/build/CMakeFiles/CMakeError.log".

By the way , could you don`t close this issue until I install apbs successfully ? Thank u very much .😭

sobolevnrm commented 2 years ago

Thank you for the detailed report. What operating system is this?

Shingzzz commented 2 years ago

Thank you for the detailed report. What operating system is this?

NAME="openEuler" VERSION="20.03 (LTS-SP3)" ID="openEuler" VERSION_ID="20.03" PRETTY_NAME="openEuler 20.03 (LTS-SP3)" ANSI_COLOR="0;31"

Linux version 4.19.90-2112.8.0.0131.oe1.aarch64

Shingzzz commented 2 years ago

hello , I try to install python3.6 , but there is a new problem:

-- Supplemental tools enabled
-- Building mesh
-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines
-- Building manip
-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines
CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
  Could NOT find Python3 (missing: Python3_LIBRARIES Python3_INCLUDE_DIRS
  Development) (found suitable exact version "3.6.9")
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:393 (_FPHSA_FAILURE_MESSAGE)
  /usr/share/cmake/Modules/FindPython/Support.cmake:2261 (find_package_handle_standard_args)
  /usr/share/cmake/Modules/FindPython3.cmake:300 (include)
  tools/python/CMakeLists.txt:12 (find_package)

It seems that I should install python3.6-devel , but I can only install python3.7-devel in this operating system , can I change the python version need for apbs ? and how to change ? please help me , thanks a lot .

alexreg commented 2 years ago

I got this issue too, except on macOS. The problem seems to be the EXACT parameter in the calls to find_package(Python3 ${PYTHON_VERSION} EXACT ..., which appear in the files CMakeLists.txt, tests/CMakeLists.txt, and tools/python/CMakeLists.txt. Removing the EXACT means it will find Python 3.6 or later, and the build seems to then succeed.

Edit: Alternatively, simply specifying -DPYTHON_VERSION=3.10 as an argument to the cmake command did the job for me. (Change to whatever Python 3.6+ version you have installed, and it should work.)

Shingzzz commented 2 years ago

I got this issue too, except on macOS. The problem seems to be the EXACT parameter in the calls to find_package(Python3 ${PYTHON_VERSION} EXACT ..., which appear in the files CMakeLists.txt, tests/CMakeLists.txt, and tools/python/CMakeLists.txt. Removing the EXACT means it will find Python 3.6 or later, and the build seems to then succeed.

Edit: Alternatively, simply specifying -DPYTHON_VERSION=3.10 as an argument to the cmake command did the job for me. (Change to whatever Python 3.6+ version you have installed, and it should work.)

thank you very much ! I solve this problem by your solution !

sobolevnrm commented 2 years ago

Thank you, @alexreg !

Shingzzz commented 2 years ago

I install apbs successfully , but when I run ctest -C Release --output-on-failure ，there are some mistakes:

83% tests passed, 3 tests failed out of 18

Total Test time (real) = 490.99 sec

The following tests FAILED:
     16 - bem_test (Failed)
     17 - bem-pKa_test (Failed)
     18 - bem-binding-energy_test (Failed)
Errors while running CTest

There are some information：

16/18 Test #16: bem_test ..................................***Failed    1.24 sec
TESTING WITH BINARY_NAME:apbs
START_DIR:/root/zqc/apbs/build
--------------------------------------------------------------------------------
Testing input file 451c_order1.in

Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.915075 seconds
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file 451c_order5.in

Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.230859 seconds
--------------------------------------------------------------------------------
Total elapsed time: 1.145934 seconds
Test results have been logged
--------------------------------------------------------------------------------
Some tests failed:  Number of test failures: 2
NOTE: Using apbs binary:/root/zqc/apbs/build/src/apbs
The following sections will be tested: bem
================================================================================
Running tests for bem section
BINARY:  /root/zqc/apbs/build/src/apbs
INPUT:   451c_order1.in
COMMAND: ['/root/zqc/apbs/build/src/apbs', '451c_order1.in']

This executable compiled on Sep 28 2022 at 20:09:33

Parsing input file 451c_order1.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from test_proteins/451c.pqr.
terminate called after throwing an instance of 'std::invalid_argument'
  what():  stoul
Checking for intermediate energies in input file 451c_order1.out
EXPECTED COMPUTED: 0
EXPECTED EXPECTED: 1
COMPUTED: []
EXPECTED: ['-4.678324477794E+03']
BINARY:  /root/zqc/apbs/build/src/apbs
INPUT:   451c_order5.in
COMMAND: ['/root/zqc/apbs/build/src/apbs', '451c_order5.in']

17/18 Test #17: bem-pKa_test ..............................***Failed    0.79 sec
TESTING WITH BINARY_NAME:apbs
START_DIR:/root/zqc/apbs/build
--------------------------------------------------------------------------------
Testing input file ASH66.in

Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.210295 seconds
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file 2LZT-ASH66.in

Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.246886 seconds
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file 2LZT-noASH66.in

Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.241297 seconds
--------------------------------------------------------------------------------
Total elapsed time: 0.698478 seconds
Test results have been logged
--------------------------------------------------------------------------------
Some tests failed:  Number of test failures: 3
NOTE: Using apbs binary:/root/zqc/apbs/build/src/apbs
The following sections will be tested: bem-pKa
================================================================================
Running tests for bem-pKa section
BINARY:  /root/zqc/apbs/build/src/apbs
INPUT:   ASH66.in
COMMAND: ['/root/zqc/apbs/build/src/apbs', 'ASH66.in']

This executable compiled on Sep 28 2022 at 20:09:33

Parsing input file ASH66.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from test_proteins/ASH66.pqr.
terminate called after throwing an instance of 'std::invalid_argument'
  what():  stoul
Checking for intermediate energies in input file ASH66.out
EXPECTED COMPUTED: 0
EXPECTED EXPECTED: 1
COMPUTED: []
EXPECTED: ['-4.005763343995E+00']
BINARY:  /root/zqc/apbs/build/src/apbs
INPUT:   2LZT-ASH66.in
COMMAND: ['/root/zqc/apbs/build/src/apbs', '2LZT-ASH66.in']

18/18 Test #18: bem-binding-energy_test ...................***Failed    0.71 sec
TESTING WITH BINARY_NAME:apbs
START_DIR:/root/zqc/apbs/build
--------------------------------------------------------------------------------
Testing input file 1d30.in

Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.2326 seconds
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file 1d30_monomer1.in

Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.197381 seconds
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file 1d30_monomer2.in

Computed result for index, 0, does not exist: list index out of rangeTest failed: list index out of range
Elapsed time: 0.184725 seconds
--------------------------------------------------------------------------------
Total elapsed time: 0.614706 seconds
Test results have been logged
--------------------------------------------------------------------------------
Some tests failed:  Number of test failures: 3
NOTE: Using apbs binary:/root/zqc/apbs/build/src/apbs
The following sections will be tested: bem-binding-energy
================================================================================
Running tests for bem-binding-energy section
BINARY:  /root/zqc/apbs/build/src/apbs
INPUT:   1d30.in
COMMAND: ['/root/zqc/apbs/build/src/apbs', '1d30.in']

This executable compiled on Sep 28 2022 at 20:09:33

Parsing input file 1d30.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from test_proteins/1d30.pqr.
terminate called after throwing an instance of 'std::invalid_argument'
  what():  stoul
Checking for intermediate energies in input file 1d30.out
EXPECTED COMPUTED: 0
EXPECTED EXPECTED: 1
COMPUTED: []
EXPECTED: ['-2.197264516397E+04']
BINARY:  /root/zqc/apbs/build/src/apbs
INPUT:   1d30_monomer1.in
COMMAND: ['/root/zqc/apbs/build/src/apbs', '1d30_monomer1.in']

I have not modified apbs/examples file . And when I run /usr/local/apbs/bin/tabipb 451c_order1.in the result: Segmentation fault (core dumped)

xiaopangjun666 commented 2 years ago

Excuse me，how did you install UMFPACK? I can't find the UMFPACK package with error when installing

Shingzzz commented 2 years ago

Excuse me，how did you install UMFPACK? I can't find the UMFPACK package with error when installing

you can install intel blas or suitesparse (and its devel) , and vim /etc/profile set LD_LIBRARY_PATH=(your install path):$LD_LIBRARY_PATH

xiaopangjun666 commented 2 years ago

Thank you very much！I find suitesparse in /usr/lib64 and set the LD_LIBRARY_PATH=/usr/lib64/:$LD_LIBRARY_PATH,but error when i try cmake again.could you tell me the reason,please image

Shingzzz commented 2 years ago

Thank you very much！I find suitesparse in /usr/lib64 and set the LD_LIBRARY_PATH=/usr/lib64/:$LD_LIBRARY_PATH,but error when i try cmake again.could you tell me the reason,please image

did you source /etc/profile ? or , you can try to install suitesparse-devel and try to cmake again . and you can echo $LD_LIBRARY_PATH , be sure that /usr/lib64 in it.