Closed acandac closed 4 years ago
davpoolechem
commented
4 years ago Hi,
Which version of GAMESS+LibCChem are you using? The build-cchem script was removed from LibCChem a while ago in favor of a CMake build system, as the build-cchem script was incredibly limited and brittle.
As for the issue you are currently running into, I would agree with you that it seems to be related to the version of the Boost install that you used.
acandac
commented
4 years ago Hi!, I downloaded gamess on January 31th, 2019. I also have a newer version downloaded sometime on February, 2020. If it makes a difference , I could install the newer version but would that change the boost installation issue? I see the same versions of boost patches in the older and newer versions.
Thanks,
davpoolechem
commented
4 years ago Hi,
Yeah, the Jan 31 version that you have would probably be before the addition of CMake to LibCChem. I would recommend using the newer version of GAMESS that you have.
As for whether that would fix the Boost issue, I think it would be worth trying at the very least, as the new build system allows LibCChem to be more amenable with newer versions of its dependency libraries such as Boost.
acandac
commented
4 years ago Hello, Thanks for helping out. I have started a fresh install of the latest version of gamess that I downloaded two days ago, February 29th, 2020. As the first step, I configured, compiled and linked the socket version of gamess. To install libcchem, I reconfigured gamess with the libcchem option, as I previously posted on this thread. I now see that ./build-cchem does not exist in /usr/local/gamess/libcchem. If build-cchem should exist after compilation, then I may have done something wrong with the installation! I see there is now LIBCCHEM_CMAKE.md and CMakeLists.txt files in /usr/local/gamess/libcchem Instructions in /usr/local/gamess/libcchem/aaa.readme.1st tells me to follow cmake installation of libcchem I installed cmake version 3.16.4 Then, execution of the following command cd /usr/local/gamess/libcchem/rysq /usr/local/cmake-3.16.4/bin/cmake ../ gives me the following error -- CMAKE_BUILD_TYPE: Release -- Detecting OpenMP with GNU CXX compiler - done -- A GPU board was not specified. GPU code is disabled. CMake Error at CMakeLists.txt:169 (message): Boost library not found! Please select a proper location for the Boost library installation. -- Configuring incomplete, errors occurred! See also "/usr/local/gamess/libcchem/rysq/CMakeFiles/CMakeOutput.log".
From the error message I see that information for libraries is not defined. I thought I defined all the library information during the second configuration of gamess. All the lib info appears to be in /usr/local/gamess/install.info Does not cmake get lib info from install.info? Do I have to redefine lib info in /usr/local/gamess/libcchem/CMakeLists.txt or something?
Best,
Jenk
davpoolechem
commented
4 years ago Hi,
You are correct that there is no more ./build-cchem script in newer versions of GAMESS. As this is the case, your installation seems to be correct based on those grounds.
Right now, the CMake build scripts for LibCChem and its associated Rys Quadrature library do not automatically pull library information from install.info, so you will need to define the locations manually. The flags that you can use for each library dependency, can be found in the LIBCCHEM_CMAKE.md file.
acandac
commented
4 years ago Hi, Thanks for the info. To make use of newer version of cmake, I uninstalled an older version of cmake and installed cmake_3.16.4. I executed cmake command using the flags below. I got the following error message during the installation, saying that rysq.hpp file does not exist.
Is there a troubleshooting to complete the installation. Regards,
Jenk
cd /usr/local/gamess/libcchem/rysq /usr/local/cmake_3.16.4/bin/cmake -DBOOST_ROOT=/usr/local/gamess-cuda-lib/boost -DGA_ROOT=/usr/local/gamess-cuda-lib/ga -DEIGEN_ROOT=/usr/local/gamess-cuda-lib/eigen -DHDF5_ROOT=/usr/local/gamess-cuda-lib/hdf5 -DGPU_BOARD=PASCAL -DMATHLIB=MKL -DMATHLIB_ROOT=/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl -DMPI_ROOT=/usr/local/openmpi ../
make && make install
make && make install Scanning dependencies of target array [ 6%] Building CXX object src/array/CMakeFiles/array.dir/hdf5.cpp.o In file included from /usr/local/gamess/libcchem/src/runtime.hpp:28:0, from /usr/local/gamess/libcchem/src/array/hdf5.cpp:1: /usr/local/gamess-cuda-lib/boost/include/boost/progress.hpp:23:108: note: #pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead. BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" ) ^ In file included from /usr/local/gamess-cuda-lib/boost/include/boost/progress.hpp:25:0, from /usr/local/gamess/libcchem/src/runtime.hpp:28, from /usr/local/gamess/libcchem/src/array/hdf5.cpp:1: /usr/local/gamess-cuda-lib/boost/include/boost/timer.hpp:21:70: note: #pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead. BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" ) ^ [ 12%] Building CXX object src/array/CMakeFiles/array.dir/memory.cpp.o [ 18%] Building CXX object src/array/CMakeFiles/array.dir/ga.cpp.o [ 18%] Built target array Scanning dependencies of target base [ 25%] Building CXX object src/CMakeFiles/base.dir/runtime.cpp.o In file included from /usr/local/gamess/libcchem/src/runtime.hpp:28:0, from /usr/local/gamess/libcchem/src/runtime.cpp:3: /usr/local/gamess-cuda-lib/boost/include/boost/progress.hpp:23:108: note: #pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead. BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" ) ^ In file included from /usr/local/gamess-cuda-lib/boost/include/boost/progress.hpp:25:0, from /usr/local/gamess/libcchem/src/runtime.hpp:28, from /usr/local/gamess/libcchem/src/runtime.cpp:3: /usr/local/gamess-cuda-lib/boost/include/boost/timer.hpp:21:70: note: #pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead. BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" ) ^ [ 25%] Built target base Scanning dependencies of target basis [ 31%] Building CXX object src/basis/CMakeFiles/basis.dir/shell.cpp.o [ 37%] Building CXX object src/basis/CMakeFiles/basis.dir/molecule.cpp.o [ 43%] Building CXX object src/basis/CMakeFiles/basis.dir/basis.cpp.o [ 43%] Built target basis Scanning dependencies of target integrals [ 50%] Building CXX object src/integrals/CMakeFiles/integrals.dir/integrals.cpp.o In file included from /usr/local/gamess/libcchem/src/integrals/integrals.cpp:2:0: /usr/local/gamess/libcchem/src/integrals/rysq.hpp:8:10: fatal error: rysq.hpp: No such file or directory
^~~~~~~~~~compilation terminated. make[2]: [src/integrals/CMakeFiles/integrals.dir/build.make:63: src/integrals/CMakeFiles/integrals.dir/integrals.cpp.o] Error 1 make[1]: [CMakeFiles/Makefile2:1049: src/integrals/CMakeFiles/integrals.dir/all] Error 2 make: *** [Makefile:141: all] Error 2
davpoolechem
commented
4 years ago Hi,
Before you install the base LibCChem install, you also want to build the associated Rys Quadrature library that comes with LibCChem. This library is present in the libcchem/rysq directory, and you can build it using CMake, as well.
acandac
commented
4 years ago Hi, Thanks for the comment. Following your instructions, I was able to compile libcchem libraries as flollows. cd /usr/local/gamess/libcchem/rysq mkdir build cd build cmake -DBOOST_ROOT=/usr/local/gamess-cuda-lib/boost -DGA_ROOT=/usr/local/gamess-cuda-lib/ga -DEIGEN_ROOT=/usr/local/gamess-cuda-lib/eigen -DHDF5_ROOT=/usr/local/gamess-cuda-lib/hdf5 -DGPU_BOARD=PASCAL -DMATHLIB=MKL -DMATHLIB_ROOT=/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl -DMPI_ROOT=/usr/local/openmpi ../
cd /usr/local/gamess/libcchem mkdir build cd build cmake -DBOOST_ROOT=/usr/local/gamess-cuda-lib/boost -DGA_ROOT=/usr/local/gamess-cuda-lib/ga -DEIGEN_ROOT=/usr/local/gamess-cuda-lib/eigen -DHDF5_ROOT=/usr/local/gamess-cuda-lib/hdf5 -DGPU_BOARD=PASCAL -DMATHLIB=MKL -DMATHLIB_ROOT=/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl -DMPI_ROOT=/usr/local/openmpi ../
ls /usr/local/gamess/libcchem/lib libcchem.a librysq.a
Then I tried to link gamess with libcchem , but got the following error message.
I think ccsd ....o files need to be installed first, and I dont know how to do that. Could you please help me out with linking gamess + libcchem ?
Best ,
./lked gamess cchem.00 Thu Mar 5 23:02:03 +03 2020 GAMESS will be linked into the binary file gamess.cchem.00.x.
The name of the linker on this machine is gfortran, and the linker options are " ".
Object code list begins "gamess.o unport.o", followed by BLAS object code " ", followed by LAPACK object code "dgeev.o dgesvd.o zheev.o", followed by VECTOR object code " ", followed by memory object code "zunix.o", followed by the standard GAMESS object code list,
aldeci.o algnci.o basccn.o basecp.o basext.o basg3l.o bashuz.o bashz2.o baskar.o basminix.o basn21.o basn31.o baspcn.o basg3x.o bassto.o casino.o ccaux.o ccddi.o ccqaux.o ccquad.o ccsdt.o ceeis.o cepa.o cnglob.o chgpen.o cimf.o ciminf.o cimi.o cimlib.o cimsub.o cisgrd.o comp.o cosmo.o cosprt.o cphf.o cpmchf.o cprohf.o cpuhf.o dccc.o dcgrd.o dcgues.o dcint2.o dclib.o dcmp2.o dcscf.o dctran.o ddilib.o delocl.o demrpt.o dft.o dftaux.o dftbfo.o dftbgr.o dftbhs.o dftblb.o dftbsk.o dftbtd.o dftbx.o dftdis.o dftfun.o dftgrd.o dftint.o dftxca.o dftxcb.o dftxcc.o dftxcd.o dftxce.o dftxcf.o dftxcg.o diab.o dmulti.o drc.o eaipcc.o ecp.o ecpder.o ecplib.o ecppot.o efpmodule.o efchtr.o efdrvr.o efelec.o efgrd2.o efgrda.o efgrdb.o efgrdc.o efinp.o efinta.o efintb.o efmo.o efmograd.o efmograd_es.o efmograd_exrep.o efmograd_disp.o efmograd_pol.o efpaul.o efpcm.o efpcov.o efpfmo.o eftei.o eigen.o elglib.o elgloc.o elgscf.o eomcc.o ewald.o excorr.o ffield.o fmo.o fmoafo.o fmocp.o fmoesd.o fmogrd.o fmoh1a.o fmoh2a.o fmoh2b.o fmoh2c.o fmohss.o fmoint.o fmoio.o fmoio_read.o fmolib.o fmomm.o fmopbc.o fmoprp.o frfmt.o fsodci.o g3.o globop.o gmcpt.o gradex.o guess.o grd1.o grd2a.o grd2b.o grd2c.o gugdga.o gugdgb.o gugdm.o gugdm2.o gugdrt.o gugem.o gugsrt.o gvb.o hess.o hss1a.o hss1b.o hss1c.o hss2a.o hss2b.o hss2c.o inputa.o inputb.o inputc.o int1.o int2a.o int2b.o int2c.o int2d.o int2f.o int2g.o int2r.o int2s.o iolib.o ivocas.o lagran.o local.o locatd.o loccd.o locpol.o locsvd.o lrd.o lut.o modmcpdft.o mcpdft.o mcpgrd.o mcpinp.o mcpint.o mcpl10.o mcpl20.o mcpl30.o mcpl40.o mcpl50.o mcpl60.o mcpl70.o mcpl80.o mccas.o mcjac.o mcqdpt.o mcqdwt.o mcqud.o mcscf.o mctwo.o mdefp.o mexing.o mltfmo.o mm23.o modmnfun.o morokm.o mnsol.o mp2.o mp2ddi.o mp2grd.o mp2gr2.o mp2ims.o mpcdat.o mpcdatpm6.o mpcgrd.o mpchbond.o mpcint.o mpcmol.o mpcmsc.o mpcpcm.o mthlib.o nameio.o nebpath.o nmr.o optcix.o ordint.o ormas1.o ormpt2.o parley.o pcm.o pcmcav.o pcmcv2.o pcmder.o pcmdis.o pcmhss.o pcmief.o pcmpol.o pcmvch.o prpamm.o prpel.o prplib.o prppop.o qeigen.o qfmm.o qmfm.o qrel.o quanpo.o raman.o reorg.o rhfuhf.o ricab.o riint.o rimp2.o rimp2omp.o rimp2grd.o rmd.o rmddat.o rmdgen.o rmdwrk.o rmdrun.o roeom.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.o secor.o sfdft.o sfgrad.o sobrt.o soffac.o solib.o sozeff.o statpt.o hrmrst.o surf.o svpchg.o svpinp.o svpleb.o symhi.o symorb.o symslc.o tddft.o tddefp.o tddfun.o tddfxc.o tddgrd.o tddint.o tddnlr.o tddxca.o tddxcc.o tddxcd_m05.o tddxcd_m06.o tddxcd_m08.o tddxcd_pkzb.o tddxcd_revtpss.o tddxcd_tpss.o tddxcd_vs98.o tddxce.o tdhf.o tdx.o tdxio.o tdxitr.o tdxni.o tdxprp.o trans.o trfdm2.o trnstn.o trudge.o umpddi.o utddft.o utdgrd.o vibanl.o vscf.o vvos.o zapddi.o zmatrx.o mod_nosp_basis.o mod_grid_storage.o mod_dft_partfunc.o mod_dft_molgrid.o mod_dft_fuzzycell.o mod_dft_gridint.o ccsd3aacgreorder.o ccsd3aacgsum.o ccsd3aacgt1A00.o ccsd3aacgt1A01.o ccsd3aacgt1A10.o ccsd3aacgt1A11.o ccsd3aacgt1A.o ccsd3aacgt1B00.o ccsd3aacgt1B01.o ccsd3aacgt1B10.o ccsd3aacgt1B11.o ccsd3aacgt1B.o ccsd3aacgt2A0000.o ccsd3aacgt2A0010.o ccsd3aacgt2A0011.o ccsd3aacgt2A1000.o ccsd3aacgt2A1010.o ccsd3aacgt2A1011.o ccsd3aacgt2A1100.o ccsd3aacgt2A1110.o ccsd3aacgt2A1111.o ccsd3aacgt2A1.o ccsd3aacgt2A.o ccsd3aacgt2B0000.o ccsd3aacgt2B0001.o ccsd3aacgt2B0010.o ccsd3aacgt2B0011.o ccsd3aacgt2B0100.o ccsd3aacgt2B0101.o ccsd3aacgt2B0110.o ccsd3aacgt2B0111.o ccsd3aacgt2B1000.o ccsd3aacgt2B1001.o ccsd3aacgt2B1010.o ccsd3aacgt2B1011.o ccsd3aacgt2B1100.o ccsd3aacgt2B1101.o ccsd3aacgt2B1110.o ccsd3aacgt2B1111.o ccsd3aacgt2B1.o ccsd3aacgt2B.o ccsd3aacgt2C0000.o ccsd3aacgt2C0010.o ccsd3aacgt2C0011.o ccsd3aacgt2C1000.o ccsd3aacgt2C1010.o ccsd3aacgt2C1011.o ccsd3aacgt2C1100.o ccsd3aacgt2C1110.o ccsd3aacgt2C1111.o ccsd3aacgt2C1.o ccsd3aacgt2C.o ccsd3aacgt3A100100.o ccsd3aacgt3A100110.o ccsd3aacgt3A100111.o ccsd3aacgt3A110100.o ccsd3aacgt3A110110.o ccsd3aacgt3A110111.o ccsd3aacgt3A111100.o ccsd3aacgt3A111110.o ccsd3aacgt3A111111.o ccsd3aacgt3AB.o ccsd3aacgt3B001001.o ccsd3aacgt3B001100.o ccsd3aacgt3B001101.o ccsd3aacgt3B001110.o ccsd3aacgt3B001111.o ccsd3aacgt3B100001.o ccsd3aacgt3B100100.o ccsd3aacgt3B100101.o ccsd3aacgt3B100110.o ccsd3aacgt3B100111.o ccsd3aacgt3B101001.o ccsd3aacgt3B101100.o ccsd3aacgt3B101101.o ccsd3aacgt3B101110.o ccsd3aacgt3B101111.o ccsd3aacgt3B110001.o ccsd3aacgt3B110100.o ccsd3aacgt3B110101.o ccsd3aacgt3B110110.o ccsd3aacgt3B110111.o ccsd3aacgt3B111001.o ccsd3aacgt3B111100.o ccsd3aacgt3B111101.o ccsd3aacgt3B111110.o ccsd3aacgt3B111111.o ccsd3aacgt3BC.o ccsd3aacgt3C010010.o ccsd3aacgt3C010011.o ccsd3aacgt3C010100.o ccsd3aacgt3C010110.o ccsd3aacgt3C010111.o ccsd3aacgt3C011010.o ccsd3aacgt3C011011.o ccsd3aacgt3C011100.o ccsd3aacgt3C011110.o ccsd3aacgt3C011111.o ccsd3aacgt3C100010.o ccsd3aacgt3C100011.o ccsd3aacgt3C100100.o ccsd3aacgt3C100110.o ccsd3aacgt3C100111.o ccsd3aacgt3C110010.o ccsd3aacgt3C110011.o ccsd3aacgt3C110100.o ccsd3aacgt3C110110.o ccsd3aacgt3C110111.o ccsd3aacgt3C111010.o ccsd3aacgt3C111011.o ccsd3aacgt3C111100.o ccsd3aacgt3C111110.o ccsd3aacgt3C111111.o ccsd3aacgt3CD.o ccsd3aacgt3D100100.o ccsd3aacgt3D100110.o ccsd3aacgt3D100111.o ccsd3aacgt3D110100.o ccsd3aacgt3D110110.o ccsd3aacgt3D110111.o ccsd3aacgt3D111100.o ccsd3aacgt3D111110.o ccsd3aacgt3D111111.o ccsd3amain.o prec.o params.o
Choices for some optional plug-in codes are Tinker/SIMOMM code skipped, using dummy file qmmm.o Both VB programs skipped, using dummy file vbdum.o Nuclear Electron Orbital code skipped, using dummy file neostb.o Using LIBCCHEM add-in C++ code for CPUs and/or Nvidia/CUDA GPUs. LIBCCHEM's libraries are cchem.o -L/usr/local/gamess/libcchem/lib -lcchem -lrysq -L/usr/local/cuda/lib64 -lcudart -lcublas -lcublas_device -lcudadevrt -L/usr/local/gamess-cuda-lib/boost_1_72_0/lib -lboost_thread -lboost_system -L/usr/local/gamess-cuda-lib/hdf5/lib64 -lhdf5 -lz -lstdc++ -lgomp -lpthread -ldl -L/usr/local/gamess-cuda-lib/libint/lib/ -lint2 Natural Bond Orbital (NBO) code skipped, using dummy file nbostb.o MPQC code skipped, using dummy file mpqcst.o
The message passing libraries searched are ga.o zga.o -lga -larmci -L/usr/local/gamess-cuda-lib/ga/lib -L/usr/local/openmpi/lib -lmpi -lmpi_mpifh
Other libraries, including math libraries, to be searched are -L/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core
Linker messages (if any) follow... dgeev.o dgesvd.o zheev.o gfortran -L/usr/local/gamess/libcchem/boost/lib -o /usr/local/gamess/gamess.cchem.00.x -I/usr/local/gamess/object gamess.o unport.o dgeev.o dgesvd.o zheev.o zunix.o aldeci.o algnci.o basccn.o basecp.o basext.o basg3l.o bashuz.o bashz2.o baskar.o basminix.o basn21.o basn31.o baspcn.o basg3x.o bassto.o casino.o ccaux.o ccddi.o ccqaux.o ccquad.o ccsdt.o ceeis.o cepa.o cnglob.o chgpen.o cimf.o ciminf.o cimi.o cimlib.o cimsub.o cisgrd.o comp.o cosmo.o cosprt.o cphf.o cpmchf.o cprohf.o cpuhf.o dccc.o dcgrd.o dcgues.o dcint2.o dclib.o dcmp2.o dcscf.o dctran.o ddilib.o delocl.o demrpt.o dft.o dftaux.o dftbfo.o dftbgr.o dftbhs.o dftblb.o dftbsk.o dftbtd.o dftbx.o dftdis.o dftfun.o dftgrd.o dftint.o dftxca.o dftxcb.o dftxcc.o dftxcd.o dftxce.o dftxcf.o dftxcg.o diab.o dmulti.o drc.o eaipcc.o ecp.o ecpder.o ecplib.o ecppot.o efpmodule.o efchtr.o efdrvr.o efelec.o efgrd2.o efgrda.o efgrdb.o efgrdc.o efinp.o efinta.o efintb.o efmo.o efmograd.o efmograd_es.o efmograd_exrep.o efmograd_disp.o efmograd_pol.o efpaul.o efpcm.o efpcov.o efpfmo.o eftei.o eigen.o elglib.o elgloc.o elgscf.o eomcc.o ewald.o excorr.o ffield.o fmo.o fmoafo.o fmocp.o fmoesd.o fmogrd.o fmoh1a.o fmoh2a.o fmoh2b.o fmoh2c.o fmohss.o fmoint.o fmoio.o fmoio_read.o fmolib.o fmomm.o fmopbc.o fmoprp.o frfmt.o fsodci.o g3.o globop.o gmcpt.o gradex.o guess.o grd1.o grd2a.o grd2b.o grd2c.o gugdga.o gugdgb.o gugdm.o gugdm2.o gugdrt.o gugem.o gugsrt.o gvb.o hess.o hss1a.o hss1b.o hss1c.o hss2a.o hss2b.o hss2c.o inputa.o inputb.o inputc.o int1.o int2a.o int2b.o int2c.o int2d.o int2f.o int2g.o int2r.o int2s.o iolib.o ivocas.o lagran.o local.o locatd.o loccd.o locpol.o locsvd.o lrd.o lut.o modmcpdft.o mcpdft.o mcpgrd.o mcpinp.o mcpint.o mcpl10.o mcpl20.o mcpl30.o mcpl40.o mcpl50.o mcpl60.o mcpl70.o mcpl80.o mccas.o mcjac.o mcqdpt.o mcqdwt.o mcqud.o mcscf.o mctwo.o mdefp.o mexing.o mltfmo.o mm23.o modmnfun.o morokm.o mnsol.o mp2.o mp2ddi.o mp2grd.o mp2gr2.o mp2ims.o mpcdat.o mpcdatpm6.o mpcgrd.o mpchbond.o mpcint.o mpcmol.o mpcmsc.o mpcpcm.o mthlib.o nameio.o nebpath.o nmr.o optcix.o ordint.o ormas1.o ormpt2.o parley.o pcm.o pcmcav.o pcmcv2.o pcmder.o pcmdis.o pcmhss.o pcmief.o pcmpol.o pcmvch.o prpamm.o prpel.o prplib.o prppop.o qeigen.o qfmm.o qmfm.o qrel.o quanpo.o raman.o reorg.o rhfuhf.o ricab.o riint.o rimp2.o rimp2omp.o rimp2grd.o rmd.o rmddat.o rmdgen.o rmdwrk.o rmdrun.o roeom.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.o secor.o sfdft.o sfgrad.o sobrt.o soffac.o solib.o sozeff.o statpt.o hrmrst.o surf.o svpchg.o svpinp.o svpleb.o symhi.o symorb.o symslc.o tddft.o tddefp.o tddfun.o tddfxc.o tddgrd.o tddint.o tddnlr.o tddxca.o tddxcc.o tddxcd_m05.o tddxcd_m06.o tddxcd_m08.o tddxcd_pkzb.o tddxcd_revtpss.o tddxcd_tpss.o tddxcd_vs98.o tddxce.o tdhf.o tdx.o tdxio.o tdxitr.o tdxni.o tdxprp.o trans.o trfdm2.o trnstn.o trudge.o umpddi.o utddft.o utdgrd.o vibanl.o vscf.o vvos.o zapddi.o zmatrx.o mod_nosp_basis.o mod_grid_storage.o mod_dft_partfunc.o mod_dft_molgrid.o mod_dft_fuzzycell.o mod_dft_gridint.o ccsd3aacgreorder.o ccsd3aacgsum.o ccsd3aacgt1A00.o ccsd3aacgt1A01.o ccsd3aacgt1A10.o ccsd3aacgt1A11.o ccsd3aacgt1A.o ccsd3aacgt1B00.o ccsd3aacgt1B01.o ccsd3aacgt1B10.o ccsd3aacgt1B11.o ccsd3aacgt1B.o ccsd3aacgt2A0000.o ccsd3aacgt2A0010.o ccsd3aacgt2A0011.o ccsd3aacgt2A1000.o ccsd3aacgt2A1010.o ccsd3aacgt2A1011.o ccsd3aacgt2A1100.o ccsd3aacgt2A1110.o ccsd3aacgt2A1111.o ccsd3aacgt2A1.o ccsd3aacgt2A.o ccsd3aacgt2B0000.o ccsd3aacgt2B0001.o ccsd3aacgt2B0010.o ccsd3aacgt2B0011.o ccsd3aacgt2B0100.o ccsd3aacgt2B0101.o ccsd3aacgt2B0110.o ccsd3aacgt2B0111.o ccsd3aacgt2B1000.o ccsd3aacgt2B1001.o ccsd3aacgt2B1010.o ccsd3aacgt2B1011.o ccsd3aacgt2B1100.o ccsd3aacgt2B1101.o ccsd3aacgt2B1110.o ccsd3aacgt2B1111.o ccsd3aacgt2B1.o ccsd3aacgt2B.o ccsd3aacgt2C0000.o ccsd3aacgt2C0010.o ccsd3aacgt2C0011.o ccsd3aacgt2C1000.o ccsd3aacgt2C1010.o ccsd3aacgt2C1011.o ccsd3aacgt2C1100.o ccsd3aacgt2C1110.o ccsd3aacgt2C1111.o ccsd3aacgt2C1.o ccsd3aacgt2C.o ccsd3aacgt3A100100.o ccsd3aacgt3A100110.o ccsd3aacgt3A100111.o ccsd3aacgt3A110100.o ccsd3aacgt3A110110.o ccsd3aacgt3A110111.o ccsd3aacgt3A111100.o ccsd3aacgt3A111110.o ccsd3aacgt3A111111.o ccsd3aacgt3AB.o ccsd3aacgt3B001001.o ccsd3aacgt3B001100.o ccsd3aacgt3B001101.o ccsd3aacgt3B001110.o ccsd3aacgt3B001111.o ccsd3aacgt3B100001.o ccsd3aacgt3B100100.o ccsd3aacgt3B100101.o ccsd3aacgt3B100110.o ccsd3aacgt3B100111.o ccsd3aacgt3B101001.o ccsd3aacgt3B101100.o ccsd3aacgt3B101101.o ccsd3aacgt3B101110.o ccsd3aacgt3B101111.o ccsd3aacgt3B110001.o ccsd3aacgt3B110100.o ccsd3aacgt3B110101.o ccsd3aacgt3B110110.o ccsd3aacgt3B110111.o ccsd3aacgt3B111001.o ccsd3aacgt3B111100.o ccsd3aacgt3B111101.o ccsd3aacgt3B111110.o ccsd3aacgt3B111111.o ccsd3aacgt3BC.o ccsd3aacgt3C010010.o ccsd3aacgt3C010011.o ccsd3aacgt3C010100.o ccsd3aacgt3C010110.o ccsd3aacgt3C010111.o ccsd3aacgt3C011010.o ccsd3aacgt3C011011.o ccsd3aacgt3C011100.o ccsd3aacgt3C011110.o ccsd3aacgt3C011111.o ccsd3aacgt3C100010.o ccsd3aacgt3C100011.o ccsd3aacgt3C100100.o ccsd3aacgt3C100110.o ccsd3aacgt3C100111.o ccsd3aacgt3C110010.o ccsd3aacgt3C110011.o ccsd3aacgt3C110100.o ccsd3aacgt3C110110.o ccsd3aacgt3C110111.o ccsd3aacgt3C111010.o ccsd3aacgt3C111011.o ccsd3aacgt3C111100.o ccsd3aacgt3C111110.o ccsd3aacgt3C111111.o ccsd3aacgt3CD.o ccsd3aacgt3D100100.o ccsd3aacgt3D100110.o ccsd3aacgt3D100111.o ccsd3aacgt3D110100.o ccsd3aacgt3D110110.o ccsd3aacgt3D110111.o ccsd3aacgt3D111100.o ccsd3aacgt3D111110.o ccsd3aacgt3D111111.o ccsd3amain.o qmmm.o vbdum.o neostb.o nbostb.o cchem.o -L/usr/local/gamess/libcchem/lib -lcchem -lrysq -L/usr/local/cuda/lib64 -lcudart -lcublas -lcublas_device -lcudadevrt -L/usr/local/gamess-cuda-lib/boost_1_72_0/lib -lboost_thread -lboost_system -L/usr/local/gamess-cuda-lib/hdf5/lib64 -lhdf5 -lz -lstdc++ -lgomp -lpthread -ldl -L/usr/local/gamess-cuda-lib/libint/lib/ -lint2 prec.o params.o mpqcst.o -L/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core -L/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core ga.o zga.o -lga -larmci -L/usr/local/gamess-cuda-lib/ga/lib -L/usr/local/openmpi/lib -lmpi -lmpi_mpifh gfortran: error: ccsd3aacgreorder.o: No such file or directory gfortran: error: ccsd3aacgsum.o: No such file or directory gfortran: error: ccsd3aacgt1A00.o: No such file or directory gfortran: error: ccsd3aacgt1A01.o: No such file or directory gfortran: error: ccsd3aacgt1A10.o: No such file or directory gfortran: error: ccsd3aacgt1A11.o: No such file or directory gfortran: error: ccsd3aacgt1A.o: No such file or directory gfortran: error: ccsd3aacgt1B00.o: No such file or directory gfortran: error: ccsd3aacgt1B01.o: No such file or directory gfortran: error: ccsd3aacgt1B10.o: No such file or directory gfortran: error: ccsd3aacgt1B11.o: No such file or directory gfortran: error: ccsd3aacgt1B.o: No such file or directory gfortran: error: ccsd3aacgt2A0000.o: No such file or directory gfortran: error: ccsd3aacgt2A0010.o: No such file or directory gfortran: error: ccsd3aacgt2A0011.o: No such file or directory gfortran: error: ccsd3aacgt2A1000.o: No such file or directory gfortran: error: ccsd3aacgt2A1010.o: No such file or directory gfortran: error: ccsd3aacgt2A1011.o: No such file or directory gfortran: error: ccsd3aacgt2A1100.o: No such file or directory gfortran: error: ccsd3aacgt2A1110.o: No such file or directory gfortran: error: ccsd3aacgt2A1111.o: No such file or directory gfortran: error: ccsd3aacgt2A1.o: No such file or directory gfortran: error: ccsd3aacgt2A.o: No such file or directory gfortran: error: ccsd3aacgt2B0000.o: No such file or directory gfortran: error: ccsd3aacgt2B0001.o: No such file or directory gfortran: error: ccsd3aacgt2B0010.o: No such file or directory gfortran: error: ccsd3aacgt2B0011.o: No such file or directory gfortran: error: ccsd3aacgt2B0100.o: No such file or directory gfortran: error: ccsd3aacgt2B0101.o: No such file or directory gfortran: error: ccsd3aacgt2B0110.o: No such file or directory gfortran: error: ccsd3aacgt2B0111.o: No such file or directory gfortran: error: ccsd3aacgt2B1000.o: No such file or directory gfortran: error: ccsd3aacgt2B1001.o: No such file or directory gfortran: error: ccsd3aacgt2B1010.o: No such file or directory gfortran: error: ccsd3aacgt2B1011.o: No such file or directory gfortran: error: ccsd3aacgt2B1100.o: No such file or directory gfortran: error: ccsd3aacgt2B1101.o: No such file or directory gfortran: error: ccsd3aacgt2B1110.o: No such file or directory gfortran: error: ccsd3aacgt2B1111.o: No such file or directory gfortran: error: ccsd3aacgt2B1.o: No such file or directory gfortran: error: ccsd3aacgt2B.o: No such file or directory gfortran: error: ccsd3aacgt2C0000.o: No such file or directory gfortran: error: ccsd3aacgt2C0010.o: No such file or directory gfortran: error: ccsd3aacgt2C0011.o: No such file or directory gfortran: error: ccsd3aacgt2C1000.o: No such file or directory gfortran: error: ccsd3aacgt2C1010.o: No such file or directory gfortran: error: ccsd3aacgt2C1011.o: No such file or directory gfortran: error: ccsd3aacgt2C1100.o: No such file or directory gfortran: error: ccsd3aacgt2C1110.o: No such file or directory gfortran: error: ccsd3aacgt2C1111.o: No such file or directory gfortran: error: ccsd3aacgt2C1.o: No such file or directory gfortran: error: ccsd3aacgt2C.o: No such file or directory gfortran: error: ccsd3aacgt3A100100.o: No such file or directory gfortran: error: ccsd3aacgt3A100110.o: No such file or directory gfortran: error: ccsd3aacgt3A100111.o: No such file or directory gfortran: error: ccsd3aacgt3A110100.o: No such file or directory gfortran: error: ccsd3aacgt3A110110.o: No such file or directory gfortran: error: ccsd3aacgt3A110111.o: No such file or directory gfortran: error: ccsd3aacgt3A111100.o: No such file or directory gfortran: error: ccsd3aacgt3A111110.o: No such file or directory gfortran: error: ccsd3aacgt3A111111.o: No such file or directory gfortran: error: ccsd3aacgt3AB.o: No such file or directory gfortran: error: ccsd3aacgt3B001001.o: No such file or directory gfortran: error: ccsd3aacgt3B001100.o: No such file or directory gfortran: error: ccsd3aacgt3B001101.o: No such file or directory gfortran: error: ccsd3aacgt3B001110.o: No such file or directory gfortran: error: ccsd3aacgt3B001111.o: No such file or directory gfortran: error: ccsd3aacgt3B100001.o: No such file or directory gfortran: error: ccsd3aacgt3B100100.o: No such file or directory gfortran: error: ccsd3aacgt3B100101.o: No such file or directory gfortran: error: ccsd3aacgt3B100110.o: No such file or directory gfortran: error: ccsd3aacgt3B100111.o: No such file or directory gfortran: error: ccsd3aacgt3B101001.o: No such file or directory gfortran: error: ccsd3aacgt3B101100.o: No such file or directory gfortran: error: ccsd3aacgt3B101101.o: No such file or directory gfortran: error: ccsd3aacgt3B101110.o: No such file or directory gfortran: error: ccsd3aacgt3B101111.o: No such file or directory gfortran: error: ccsd3aacgt3B110001.o: No such file or directory gfortran: error: ccsd3aacgt3B110100.o: No such file or directory gfortran: error: ccsd3aacgt3B110101.o: No such file or directory gfortran: error: ccsd3aacgt3B110110.o: No such file or directory gfortran: error: ccsd3aacgt3B110111.o: No such file or directory gfortran: error: ccsd3aacgt3B111001.o: No such file or directory gfortran: error: ccsd3aacgt3B111100.o: No such file or directory gfortran: error: ccsd3aacgt3B111101.o: No such file or directory gfortran: error: ccsd3aacgt3B111110.o: No such file or directory gfortran: error: ccsd3aacgt3B111111.o: No such file or directory gfortran: error: ccsd3aacgt3BC.o: No such file or directory gfortran: error: ccsd3aacgt3C010010.o: No such file or directory gfortran: error: ccsd3aacgt3C010011.o: No such file or directory gfortran: error: ccsd3aacgt3C010100.o: No such file or directory gfortran: error: ccsd3aacgt3C010110.o: No such file or directory gfortran: error: ccsd3aacgt3C010111.o: No such file or directory gfortran: error: ccsd3aacgt3C011010.o: No such file or directory gfortran: error: ccsd3aacgt3C011011.o: No such file or directory gfortran: error: ccsd3aacgt3C011100.o: No such file or directory gfortran: error: ccsd3aacgt3C011110.o: No such file or directory gfortran: error: ccsd3aacgt3C011111.o: No such file or directory gfortran: error: ccsd3aacgt3C100010.o: No such file or directory gfortran: error: ccsd3aacgt3C100011.o: No such file or directory gfortran: error: ccsd3aacgt3C100100.o: No such file or directory gfortran: error: ccsd3aacgt3C100110.o: No such file or directory gfortran: error: ccsd3aacgt3C100111.o: No such file or directory gfortran: error: ccsd3aacgt3C110010.o: No such file or directory gfortran: error: ccsd3aacgt3C110011.o: No such file or directory gfortran: error: ccsd3aacgt3C110100.o: No such file or directory gfortran: error: ccsd3aacgt3C110110.o: No such file or directory gfortran: error: ccsd3aacgt3C110111.o: No such file or directory gfortran: error: ccsd3aacgt3C111010.o: No such file or directory gfortran: error: ccsd3aacgt3C111011.o: No such file or directory gfortran: error: ccsd3aacgt3C111100.o: No such file or directory gfortran: error: ccsd3aacgt3C111110.o: No such file or directory gfortran: error: ccsd3aacgt3C111111.o: No such file or directory gfortran: error: ccsd3aacgt3CD.o: No such file or directory gfortran: error: ccsd3aacgt3D100100.o: No such file or directory gfortran: error: ccsd3aacgt3D100110.o: No such file or directory gfortran: error: ccsd3aacgt3D100111.o: No such file or directory gfortran: error: ccsd3aacgt3D110100.o: No such file or directory gfortran: error: ccsd3aacgt3D110110.o: No such file or directory gfortran: error: ccsd3aacgt3D110111.o: No such file or directory gfortran: error: ccsd3aacgt3D111100.o: No such file or directory gfortran: error: ccsd3aacgt3D111110.o: No such file or directory gfortran: error: ccsd3aacgt3D111111.o: No such file or directory gfortran: error: ccsd3amain.o: No such file or directory gfortran: error: cchem.o: No such file or directory gfortran: error: ga.o: No such file or directory gfortran: error: zga.o: No such file or directory set rc=1 unset echo
Unfortunately, there was an error while linking GAMESS. 0.028u 0.026s 0:00.05 80.0% 0+0k 0+0io 0pf+0w
davpoolechem
commented
4 years ago Hi,
I'm glad to hear that LibCChem built successfully for you!
As for linking GAMESS+LibCChem, you don't necessarily have to build those coupled-cluster files. If you rerun the config script for GAMESS, there will be an option asking you if you want to build the Michigan State Coupled-Cluster code. Select "no" for this, and rebuild. Then, you won't have any issues with the missing CC code seen here. Alternatively, to do this without rerunning config, you can go into the install.info and Makefile files and switch the value of the GMS_MSUCC variable to "false".
It also seems you ran into some issues regarding the GAMESS+LibCChem interface files (cchem, ga, and zga). For cchem and ga, you can compile these using the "./comp cchem" and "./comp ga" commands, respectively, in the command line. For zga, you can compile this using "gcc -c source/zga.c" and moving the resulting zga.o object file to the object/ directory.
Then try relinking and see what happens.
acandac
commented
4 years ago Hi, Following your comments I was able to solve the GMS_MSUCC, zga, ga and chcem issues. Thank you! After reconfiguration, I tried to re-link GAMESS with LibCChem, and got a new error message. I will appreciate it much if you could comment on a solution to the following error message as well.
Best,
./lked gamess cchem.00 Sun Mar 8 13:16:58 +03 2020 GAMESS will be linked into the binary file gamess.cchem.00.x.
The name of the linker on this machine is gfortran, and the linker options are " ".
Object code list begins "gamess.o unport.o", followed by BLAS object code " ", followed by LAPACK object code "dgeev.o dgesvd.o zheev.o", followed by VECTOR object code " ", followed by memory object code "zunix.o", followed by the standard GAMESS object code list,
aldeci.o algnci.o basccn.o basecp.o basext.o basg3l.o bashuz.o bashz2.o baskar.o basminix.o basn21.o basn31.o baspcn.o basg3x.o bassto.o casino.o ccaux.o ccddi.o ccqaux.o ccquad.o ccsdt.o ceeis.o cepa.o cnglob.o chgpen.o cimf.o ciminf.o cimi.o cimlib.o cimsub.o cisgrd.o comp.o cosmo.o cosprt.o cphf.o cpmchf.o cprohf.o cpuhf.o dccc.o dcgrd.o dcgues.o dcint2.o dclib.o dcmp2.o dcscf.o dctran.o ddilib.o delocl.o demrpt.o dft.o dftaux.o dftbfo.o dftbgr.o dftbhs.o dftblb.o dftbsk.o dftbtd.o dftbx.o dftdis.o dftfun.o dftgrd.o dftint.o dftxca.o dftxcb.o dftxcc.o dftxcd.o dftxce.o dftxcf.o dftxcg.o diab.o dmulti.o drc.o eaipcc.o ecp.o ecpder.o ecplib.o ecppot.o efpmodule.o efchtr.o efdrvr.o efelec.o efgrd2.o efgrda.o efgrdb.o efgrdc.o efinp.o efinta.o efintb.o efmo.o efmograd.o efmograd_es.o efmograd_exrep.o efmograd_disp.o efmograd_pol.o efpaul.o efpcm.o efpcov.o efpfmo.o eftei.o eigen.o elglib.o elgloc.o elgscf.o eomcc.o ewald.o excorr.o ffield.o fmo.o fmoafo.o fmocp.o fmoesd.o fmogrd.o fmoh1a.o fmoh2a.o fmoh2b.o fmoh2c.o fmohss.o fmoint.o fmoio.o fmoio_read.o fmolib.o fmomm.o fmopbc.o fmoprp.o frfmt.o fsodci.o g3.o globop.o gmcpt.o gradex.o guess.o grd1.o grd2a.o grd2b.o grd2c.o gugdga.o gugdgb.o gugdm.o gugdm2.o gugdrt.o gugem.o gugsrt.o gvb.o hess.o hss1a.o hss1b.o hss1c.o hss2a.o hss2b.o hss2c.o inputa.o inputb.o inputc.o int1.o int2a.o int2b.o int2c.o int2d.o int2f.o int2g.o int2r.o int2s.o iolib.o ivocas.o lagran.o local.o locatd.o loccd.o locpol.o locsvd.o lrd.o lut.o modmcpdft.o mcpdft.o mcpgrd.o mcpinp.o mcpint.o mcpl10.o mcpl20.o mcpl30.o mcpl40.o mcpl50.o mcpl60.o mcpl70.o mcpl80.o mccas.o mcjac.o mcqdpt.o mcqdwt.o mcqud.o mcscf.o mctwo.o mdefp.o mexing.o mltfmo.o mm23.o modmnfun.o morokm.o mnsol.o mp2.o mp2ddi.o mp2grd.o mp2gr2.o mp2ims.o mpcdat.o mpcdatpm6.o mpcgrd.o mpchbond.o mpcint.o mpcmol.o mpcmsc.o mpcpcm.o mthlib.o nameio.o nebpath.o nmr.o optcix.o ordint.o ormas1.o ormpt2.o parley.o pcm.o pcmcav.o pcmcv2.o pcmder.o pcmdis.o pcmhss.o pcmief.o pcmpol.o pcmvch.o prpamm.o prpel.o prplib.o prppop.o qeigen.o qfmm.o qmfm.o qrel.o quanpo.o raman.o reorg.o rhfuhf.o ricab.o riint.o rimp2.o rimp2omp.o rimp2grd.o rmd.o rmddat.o rmdgen.o rmdwrk.o rmdrun.o roeom.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.o secor.o sfdft.o sfgrad.o sobrt.o soffac.o solib.o sozeff.o statpt.o hrmrst.o surf.o svpchg.o svpinp.o svpleb.o symhi.o symorb.o symslc.o tddft.o tddefp.o tddfun.o tddfxc.o tddgrd.o tddint.o tddnlr.o tddxca.o tddxcc.o tddxcd_m05.o tddxcd_m06.o tddxcd_m08.o tddxcd_pkzb.o tddxcd_revtpss.o tddxcd_tpss.o tddxcd_vs98.o tddxce.o tdhf.o tdx.o tdxio.o tdxitr.o tdxni.o tdxprp.o trans.o trfdm2.o trnstn.o trudge.o umpddi.o utddft.o utdgrd.o vibanl.o vscf.o vvos.o zapddi.o zmatrx.o mod_nosp_basis.o mod_grid_storage.o mod_dft_partfunc.o mod_dft_molgrid.o mod_dft_fuzzycell.o mod_dft_gridint.o stubcc3.o prec.o params.o
Choices for some optional plug-in codes are Tinker/SIMOMM code skipped, using dummy file qmmm.o Both VB programs skipped, using dummy file vbdum.o Nuclear Electron Orbital code skipped, using dummy file neostb.o Using LIBCCHEM add-in C++ code for CPUs and/or Nvidia/CUDA GPUs. LIBCCHEM's libraries are cchem.o -L/usr/local/gamess/libcchem/lib -lcchem -lrysq -L/usr/local/cuda/lib64 -lcudart -lcublas -lcublas_device -lcudadevrt -L/usr/local/gamess-cuda-lib/boost_1_72_0/lib -lboost_thread -lboost_system -L/usr/local/gamess-cuda-lib/hdf5/lib64 -lhdf5 -lz -lstdc++ -lgomp -lpthread -ldl -L/usr/local/gamess-cuda-lib/libint/lib/ -lint2 Natural Bond Orbital (NBO) code skipped, using dummy file nbostb.o MPQC code skipped, using dummy file mpqcst.o
The message passing libraries searched are ga.o zga.o -lga -larmci -L/usr/local/gamess-cuda-lib/ga/lib -L/usr/local/openmpi/lib -lmpi -lmpi_mpifh
Other libraries, including math libraries, to be searched are -L/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core
Linker messages (if any) follow...
dgeev.o dgesvd.o zheev.o
gfortran -L/usr/local/gamess/libcchem/boost/lib -o /usr/local/gamess/gamess.cchem.00.x -I/usr/local/gamess/object gamess.o unport.o dgeev.o dgesvd.o zheev.o zunix.o aldeci.o algnci.o basccn.o basecp.o basext.o basg3l.o bashuz.o bashz2.o baskar.o basminix.o basn21.o basn31.o baspcn.o basg3x.o bassto.o casino.o ccaux.o ccddi.o ccqaux.o ccquad.o ccsdt.o ceeis.o cepa.o cnglob.o chgpen.o cimf.o ciminf.o cimi.o cimlib.o cimsub.o cisgrd.o comp.o cosmo.o cosprt.o cphf.o cpmchf.o cprohf.o cpuhf.o dccc.o dcgrd.o dcgues.o dcint2.o dclib.o dcmp2.o dcscf.o dctran.o ddilib.o delocl.o demrpt.o dft.o dftaux.o dftbfo.o dftbgr.o dftbhs.o dftblb.o dftbsk.o dftbtd.o dftbx.o dftdis.o dftfun.o dftgrd.o dftint.o dftxca.o dftxcb.o dftxcc.o dftxcd.o dftxce.o dftxcf.o dftxcg.o diab.o dmulti.o drc.o eaipcc.o ecp.o ecpder.o ecplib.o ecppot.o efpmodule.o efchtr.o efdrvr.o efelec.o efgrd2.o efgrda.o efgrdb.o efgrdc.o efinp.o efinta.o efintb.o efmo.o efmograd.o efmograd_es.o efmograd_exrep.o efmograd_disp.o efmograd_pol.o efpaul.o efpcm.o efpcov.o efpfmo.o eftei.o eigen.o elglib.o elgloc.o elgscf.o eomcc.o ewald.o excorr.o ffield.o fmo.o fmoafo.o fmocp.o fmoesd.o fmogrd.o fmoh1a.o fmoh2a.o fmoh2b.o fmoh2c.o fmohss.o fmoint.o fmoio.o fmoio_read.o fmolib.o fmomm.o fmopbc.o fmoprp.o frfmt.o fsodci.o g3.o globop.o gmcpt.o gradex.o guess.o grd1.o grd2a.o grd2b.o grd2c.o gugdga.o gugdgb.o gugdm.o gugdm2.o gugdrt.o gugem.o gugsrt.o gvb.o hess.o hss1a.o hss1b.o hss1c.o hss2a.o hss2b.o hss2c.o inputa.o inputb.o inputc.o int1.o int2a.o int2b.o int2c.o int2d.o int2f.o int2g.o int2r.o int2s.o iolib.o ivocas.o lagran.o local.o locatd.o loccd.o locpol.o locsvd.o lrd.o lut.o modmcpdft.o mcpdft.o mcpgrd.o mcpinp.o mcpint.o mcpl10.o mcpl20.o mcpl30.o mcpl40.o mcpl50.o mcpl60.o mcpl70.o mcpl80.o mccas.o mcjac.o mcqdpt.o mcqdwt.o mcqud.o mcscf.o mctwo.o mdefp.o mexing.o mltfmo.o mm23.o modmnfun.o morokm.o mnsol.o mp2.o mp2ddi.o mp2grd.o mp2gr2.o mp2ims.o mpcdat.o mpcdatpm6.o mpcgrd.o mpchbond.o mpcint.o mpcmol.o mpcmsc.o mpcpcm.o mthlib.o nameio.o nebpath.o nmr.o optcix.o ordint.o ormas1.o ormpt2.o parley.o pcm.o pcmcav.o pcmcv2.o pcmder.o pcmdis.o pcmhss.o pcmief.o pcmpol.o pcmvch.o prpamm.o prpel.o prplib.o prppop.o qeigen.o qfmm.o qmfm.o qrel.o quanpo.o raman.o reorg.o rhfuhf.o ricab.o riint.o rimp2.o rimp2omp.o rimp2grd.o rmd.o rmddat.o rmdgen.o rmdwrk.o rmdrun.o roeom.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.o secor.o sfdft.o sfgrad.o sobrt.o soffac.o solib.o sozeff.o statpt.o hrmrst.o surf.o svpchg.o svpinp.o svpleb.o symhi.o symorb.o symslc.o tddft.o tddefp.o tddfun.o tddfxc.o tddgrd.o tddint.o tddnlr.o tddxca.o tddxcc.o tddxcd_m05.o tddxcd_m06.o tddxcd_m08.o tddxcd_pkzb.o tddxcd_revtpss.o tddxcd_tpss.o tddxcd_vs98.o tddxce.o tdhf.o tdx.o tdxio.o tdxitr.o tdxni.o tdxprp.o trans.o trfdm2.o trnstn.o trudge.o umpddi.o utddft.o utdgrd.o vibanl.o vscf.o vvos.o zapddi.o zmatrx.o mod_nosp_basis.o mod_grid_storage.o mod_dft_partfunc.o mod_dft_molgrid.o mod_dft_fuzzycell.o mod_dft_gridint.o stubcc3.o qmmm.o vbdum.o neostb.o nbostb.o cchem.o -L/usr/local/gamess/libcchem/lib -lcchem -lrysq -L/usr/local/cuda/lib64 -lcudart -lcublas -lcublas_device -lcudadevrt -L/usr/local/gamess-cuda-lib/boost_1_72_0/lib -lboost_thread -lboost_system -L/usr/local/gamess-cuda-lib/hdf5/lib64 -lhdf5 -lz -lstdc++ -lgomp -lpthread -ldl -L/usr/local/gamess-cuda-lib/libint/lib/ -lint2 prec.o params.o mpqcst.o -L/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core -L/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core ga.o zga.o -lga -larmci -L/usr/local/gamess-cuda-lib/ga/lib -L/usr/local/openmpi/lib -lmpi -lmpi_mpifh
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: cchem.o: in function gms_cchem_hf_fock_': /usr/local/gamess/object/cchem.F:165: undefined reference tocchem_hffock'
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: cchem.o: in function gms_cchem_mp2_energy_': /usr/local/gamess/object/cchem.F:268: undefined reference tocchem_mp2energy'
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: cchem.o: in function gms_cchem_ri_mp2_': /usr/local/gamess/object/cchem.F:557: undefined reference tocchem_rimp2gradient'
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: /usr/local/gamess/object/cchem.F:552: undefined reference to cchem_rimp2_energy_' /usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: cchem.o: in functiongms_cchem_dfrhf':
/usr/local/gamess/object/cchem.F:810: undefined reference to cchem_df_rhf_' /usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: cchem.o: in functiongms_cchem_ccsdenergy':
/usr/local/gamess/object/cchem.F:1205: undefined reference to cchem_cc_energy_' /usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: ga.o: in functionddipbeg':
/usr/local/gamess/object/ga.F:400: undefined reference to `gamess_mpiinit'
collect2: error: ld returned 1 exit status
set rc=1
unset echo
Unfortunately, there was an error while linking GAMESS. 0.970u 0.205s 0:01.17 100.0% 0+0k 0+351912io 0pf+0w
acandac
commented
4 years ago Hi again! Hoping that the following info may help in figuring out the problem in my previous message . Best,
./comp cchem ======================== cchem ============================== Sun Mar 8 13:47:19 +03 2020 Copying source code, cchem.src does not require activation. gfortran -c -fdefault-integer-8 -g -ffpe-trap=invalid,zero,overflow -O2 -DHAVE_CCHEM -DBUILD_HF -DBUILD_MP2 -DBUILD_RI -DBUILD_CC -w -fno-aggressive-loop-optimizations -funconstrained-commons cchem.F unset echo Sun Mar 8 13:47:19 +03 2020 0.214u 0.013s 0:00.22 100.0% 0+0k 0+1472io 0pf+0w ./comp ga ======================== ga ============================== Sun Mar 8 13:47:43 +03 2020 Copying source code, ga.src does not require activation. gfortran -c -fdefault-integer-8 -g -ffpe-trap=invalid,zero,overflow -O2 -std=legacy -I/usr/local/gamess-cuda-lib/ga/include -w -fno-aggressive-loop-optimizations -funconstrained-commons ga.F unset echo Sun Mar 8 13:47:43 +03 2020 0.174u 0.018s 0:00.19 94.7% 0+0k 0+872io 0pf+0w
colleeneb
commented
4 years ago To me, the error output looks like libcchem.a isn’t getting linked in properly, or something is wrong with it (the undefined references (undefined reference to cchem_hf_fock_') are to functions in libcchem).
First, could you check that “/usr/local/gamess/libcchem/lib/libcchem.a” exists, and if it does then run
$ nm /usr/local/gamess/libcchem/lib/libcchem.a | grep cchem_hf_fockDoes anything come out? If you see a result, but it doesn’t have the underscore after it (cchem_hf_fock_), then it might mean there’s a missing underscore flag somewhere. In the meantime, I’ll try to reproduce.
colleeneb
commented
4 years ago Ok, I was able to reproduce. It looks like you'll need to pass -DBUILD_HF=1 -DBUILD_RI=1 to the compilation of librysq and -DBUILD_ALL=1 to building libcchem.a.
FWIW, my steps were:
# configured GAMESS without MSU CC and without libcchem
# compiled without libcchem:
$ make ddi
$ make modules
$ make -j56This compiled non-libcchem GAMESS ok.
Then to get libcchem:
$ cd libcchemI used the following build script:
module load gcc/7.4.0
module load cuda
module load cmake
module load intel
module load mpi
set -x
make clean
rm -rf lib/*
rm -rf rysq/build/
mkdir -p rysq/build/
cd rysq/build/
CC=gcc CXX=g++ cmake \
-DBUILD_HF=1 \
-DBUILD_RI=1 \
-DCMAKE_BUILD_TYPE=Debug \
-DGPU_BOARD=VOLTA \
-DBOOST_ROOT=/home/bertoni/opt/boost/ \
../
make -j48
make install
cd ../..
rm -rf build
mkdir build
cd build
CC=gcc CXX=g++ cmake \
-DBUILD_ALL=1 \
-DCMAKE_BUILD_TYPE=Debug \
-DEIGEN_ROOT=/home/bertoni/opt/eigen/ \
-DHDF5_ROOT=/home/bertoni/opt/hdf5/ \
-DGPU_BOARD=VOLTA \
-DMATHLIB=MKL \
-DMATHLIB_ROOT=${MKLROOT} \
-DMPI_ROOT=${I_MPI_ROOT} \
-DBOOST_ROOT=/home/bertoni/opt/boost/ \
-DGA_ROOT=/home/bertoni/gpu_tests/cp11/gamess/libcchem/externals/ga/ \
../
make -j48
make installthen:
# rerun ./config and say yes to libcchem, enter in the paths to eigen, boost, etc. that were used in cmake before
# make sure to use a different version number here than before so you can distinguish
# between this version and the non-libcchem veersion
$ make
# and it compiledEdit: if you see an error about cublasdevice not found, you can comment it out from lked
acandac
commented
4 years ago Hi,
Thanks for the comment.
"First, could you check that “/usr/local/gamess/libcchem/lib/libcchem.a” exists, and if it does then run $ nm /usr/local/gamess/libcchem/lib/libcchem.a | grep cchem_hf_fock Does anything come out?" Tried it, unfortunately nothing comes out.
I'll go through your next comments now..
Thank you for your help
acandac
commented
4 years ago Hi again! I followed your instructions on rebuilding rysq and cchem libraries. Here is the result of nm libcchem.a | grep cchem_hf_fock 00000000000005b0 T cchem_hffock seems like OK . "# rerun ./config and say yes to libcchem, enter in the paths to eigen, boost, etc. that were used in cmake before $ make " I did this as well . gamess compiled with no error messages. Make then attempted to link gamess with libcchem. Below is the error message I got. Any suggestion that you make to solve this problem will be greatly appreciated. Thanks,
GAMESS will be linked into the binary file gamess.00.x.
The name of the linker on this machine is gfortran, and the linker options are " ".
Object code list begins "gamess.o unport.o", followed by BLAS object code " ", followed by LAPACK object code "dgeev.o dgesvd.o zheev.o", followed by VECTOR object code " ", followed by memory object code "zunix.o", followed by the standard GAMESS object code list,
aldeci.o algnci.o basccn.o basecp.o basext.o basg3l.o bashuz.o bashz2.o baskar.o basminix.o basn21.o basn31.o baspcn.o basg3x.o bassto.o casino.o ccaux.o ccddi.o ccqaux.o ccquad.o ccsdt.o ceeis.o cepa.o cnglob.o chgpen.o cimf.o ciminf.o cimi.o cimlib.o cimsub.o cisgrd.o comp.o cosmo.o cosprt.o cphf.o cpmchf.o cprohf.o cpuhf.o dccc.o dcgrd.o dcgues.o dcint2.o dclib.o dcmp2.o dcscf.o dctran.o ddilib.o delocl.o demrpt.o dft.o dftaux.o dftbfo.o dftbgr.o dftbhs.o dftblb.o dftbsk.o dftbtd.o dftbx.o dftdis.o dftfun.o dftgrd.o dftint.o dftxca.o dftxcb.o dftxcc.o dftxcd.o dftxce.o dftxcf.o dftxcg.o diab.o dmulti.o drc.o eaipcc.o ecp.o ecpder.o ecplib.o ecppot.o efpmodule.o efchtr.o efdrvr.o efelec.o efgrd2.o efgrda.o efgrdb.o efgrdc.o efinp.o efinta.o efintb.o efmo.o efmograd.o efmograd_es.o efmograd_exrep.o efmograd_disp.o efmograd_pol.o efpaul.o efpcm.o efpcov.o efpfmo.o eftei.o eigen.o elglib.o elgloc.o elgscf.o eomcc.o ewald.o excorr.o ffield.o fmo.o fmoafo.o fmocp.o fmoesd.o fmogrd.o fmoh1a.o fmoh2a.o fmoh2b.o fmoh2c.o fmohss.o fmoint.o fmoio.o fmoio_read.o fmolib.o fmomm.o fmopbc.o fmoprp.o frfmt.o fsodci.o g3.o globop.o gmcpt.o gradex.o guess.o grd1.o grd2a.o grd2b.o grd2c.o gugdga.o gugdgb.o gugdm.o gugdm2.o gugdrt.o gugem.o gugsrt.o gvb.o hess.o hss1a.o hss1b.o hss1c.o hss2a.o hss2b.o hss2c.o inputa.o inputb.o inputc.o int1.o int2a.o int2b.o int2c.o int2d.o int2f.o int2g.o int2r.o int2s.o iolib.o ivocas.o lagran.o local.o locatd.o loccd.o locpol.o locsvd.o lrd.o lut.o modmcpdft.o mcpdft.o mcpgrd.o mcpinp.o mcpint.o mcpl10.o mcpl20.o mcpl30.o mcpl40.o mcpl50.o mcpl60.o mcpl70.o mcpl80.o mccas.o mcjac.o mcqdpt.o mcqdwt.o mcqud.o mcscf.o mctwo.o mdefp.o mexing.o mltfmo.o mm23.o modmnfun.o morokm.o mnsol.o mp2.o mp2ddi.o mp2grd.o mp2gr2.o mp2ims.o mpcdat.o mpcdatpm6.o mpcgrd.o mpchbond.o mpcint.o mpcmol.o mpcmsc.o mpcpcm.o mthlib.o nameio.o nebpath.o nmr.o optcix.o ordint.o ormas1.o ormpt2.o parley.o pcm.o pcmcav.o pcmcv2.o pcmder.o pcmdis.o pcmhss.o pcmief.o pcmpol.o pcmvch.o prpamm.o prpel.o prplib.o prppop.o qeigen.o qfmm.o qmfm.o qrel.o quanpo.o raman.o reorg.o rhfuhf.o ricab.o riint.o rimp2.o rimp2omp.o rimp2grd.o rmd.o rmddat.o rmdgen.o rmdwrk.o rmdrun.o roeom.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.o secor.o sfdft.o sfgrad.o sobrt.o soffac.o solib.o sozeff.o statpt.o hrmrst.o surf.o svpchg.o svpinp.o svpleb.o symhi.o symorb.o symslc.o tddft.o tddefp.o tddfun.o tddfxc.o tddgrd.o tddint.o tddnlr.o tddxca.o tddxcc.o tddxcd_m05.o tddxcd_m06.o tddxcd_m08.o tddxcd_pkzb.o tddxcd_revtpss.o tddxcd_tpss.o tddxcd_vs98.o tddxce.o tdhf.o tdx.o tdxio.o tdxitr.o tdxni.o tdxprp.o trans.o trfdm2.o trnstn.o trudge.o umpddi.o utddft.o utdgrd.o vibanl.o vscf.o vvos.o zapddi.o zmatrx.o mod_nosp_basis.o mod_grid_storage.o mod_dft_partfunc.o mod_dft_molgrid.o mod_dft_fuzzycell.o mod_dft_gridint.o stubcc3.o prec.o params.o
Choices for some optional plug-in codes are Tinker/SIMOMM code skipped, using dummy file qmmm.o Both VB programs skipped, using dummy file vbdum.o Nuclear Electron Orbital code skipped, using dummy file neostb.o Using LIBCCHEM add-in C++ code for CPUs and/or Nvidia/CUDA GPUs. LIBCCHEM's libraries are cchem.o -L/usr/local/gamess/libcchem/lib -lcchem -lrysq -L/usr/local/cuda/lib64 -lcudart -lcublas -lcublas_device -lcudadevrt -L/usr/local/gamess-cuda-lib/boost_1_72_0/lib -lboost_thread -lboost_system -L/usr/local/gamess-cuda-lib/hdf5/lib64 -lhdf5 -lz -lstdc++ -lgomp -lpthread -ldl -L/usr/local/gamess-cuda-lib/libint/lib/ -lint2 Natural Bond Orbital (NBO) code skipped, using dummy file nbostb.o MPQC code skipped, using dummy file mpqcst.o
The message passing libraries searched are ga.o zga.o -lga -larmci -L/usr/local/gamess-cuda-lib/ga/lib -L/usr/local/openmpi/lib -lmpi -lmpi_mpifh
Other libraries, including math libraries, to be searched are -L/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core
Linker messages (if any) follow...
dgeev.o dgesvd.o zheev.o
gfortran -L/usr/local/gamess/libcchem/boost/lib -o /usr/local/gamess/gamess.00.x -I/usr/local/gamess/object gamess.o unport.o dgeev.o dgesvd.o zheev.o zunix.o aldeci.o algnci.o basccn.o basecp.o basext.o basg3l.o bashuz.o bashz2.o baskar.o basminix.o basn21.o basn31.o baspcn.o basg3x.o bassto.o casino.o ccaux.o ccddi.o ccqaux.o ccquad.o ccsdt.o ceeis.o cepa.o cnglob.o chgpen.o cimf.o ciminf.o cimi.o cimlib.o cimsub.o cisgrd.o comp.o cosmo.o cosprt.o cphf.o cpmchf.o cprohf.o cpuhf.o dccc.o dcgrd.o dcgues.o dcint2.o dclib.o dcmp2.o dcscf.o dctran.o ddilib.o delocl.o demrpt.o dft.o dftaux.o dftbfo.o dftbgr.o dftbhs.o dftblb.o dftbsk.o dftbtd.o dftbx.o dftdis.o dftfun.o dftgrd.o dftint.o dftxca.o dftxcb.o dftxcc.o dftxcd.o dftxce.o dftxcf.o dftxcg.o diab.o dmulti.o drc.o eaipcc.o ecp.o ecpder.o ecplib.o ecppot.o efpmodule.o efchtr.o efdrvr.o efelec.o efgrd2.o efgrda.o efgrdb.o efgrdc.o efinp.o efinta.o efintb.o efmo.o efmograd.o efmograd_es.o efmograd_exrep.o efmograd_disp.o efmograd_pol.o efpaul.o efpcm.o efpcov.o efpfmo.o eftei.o eigen.o elglib.o elgloc.o elgscf.o eomcc.o ewald.o excorr.o ffield.o fmo.o fmoafo.o fmocp.o fmoesd.o fmogrd.o fmoh1a.o fmoh2a.o fmoh2b.o fmoh2c.o fmohss.o fmoint.o fmoio.o fmoio_read.o fmolib.o fmomm.o fmopbc.o fmoprp.o frfmt.o fsodci.o g3.o globop.o gmcpt.o gradex.o guess.o grd1.o grd2a.o grd2b.o grd2c.o gugdga.o gugdgb.o gugdm.o gugdm2.o gugdrt.o gugem.o gugsrt.o gvb.o hess.o hss1a.o hss1b.o hss1c.o hss2a.o hss2b.o hss2c.o inputa.o inputb.o inputc.o int1.o int2a.o int2b.o int2c.o int2d.o int2f.o int2g.o int2r.o int2s.o iolib.o ivocas.o lagran.o local.o locatd.o loccd.o locpol.o locsvd.o lrd.o lut.o modmcpdft.o mcpdft.o mcpgrd.o mcpinp.o mcpint.o mcpl10.o mcpl20.o mcpl30.o mcpl40.o mcpl50.o mcpl60.o mcpl70.o mcpl80.o mccas.o mcjac.o mcqdpt.o mcqdwt.o mcqud.o mcscf.o mctwo.o mdefp.o mexing.o mltfmo.o mm23.o modmnfun.o morokm.o mnsol.o mp2.o mp2ddi.o mp2grd.o mp2gr2.o mp2ims.o mpcdat.o mpcdatpm6.o mpcgrd.o mpchbond.o mpcint.o mpcmol.o mpcmsc.o mpcpcm.o mthlib.o nameio.o nebpath.o nmr.o optcix.o ordint.o ormas1.o ormpt2.o parley.o pcm.o pcmcav.o pcmcv2.o pcmder.o pcmdis.o pcmhss.o pcmief.o pcmpol.o pcmvch.o prpamm.o prpel.o prplib.o prppop.o qeigen.o qfmm.o qmfm.o qrel.o quanpo.o raman.o reorg.o rhfuhf.o ricab.o riint.o rimp2.o rimp2omp.o rimp2grd.o rmd.o rmddat.o rmdgen.o rmdwrk.o rmdrun.o roeom.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.o secor.o sfdft.o sfgrad.o sobrt.o soffac.o solib.o sozeff.o statpt.o hrmrst.o surf.o svpchg.o svpinp.o svpleb.o symhi.o symorb.o symslc.o tddft.o tddefp.o tddfun.o tddfxc.o tddgrd.o tddint.o tddnlr.o tddxca.o tddxcc.o tddxcd_m05.o tddxcd_m06.o tddxcd_m08.o tddxcd_pkzb.o tddxcd_revtpss.o tddxcd_tpss.o tddxcd_vs98.o tddxce.o tdhf.o tdx.o tdxio.o tdxitr.o tdxni.o tdxprp.o trans.o trfdm2.o trnstn.o trudge.o umpddi.o utddft.o utdgrd.o vibanl.o vscf.o vvos.o zapddi.o zmatrx.o mod_nosp_basis.o mod_grid_storage.o mod_dft_partfunc.o mod_dft_molgrid.o mod_dft_fuzzycell.o mod_dft_gridint.o stubcc3.o qmmm.o vbdum.o neostb.o nbostb.o cchem.o -L/usr/local/gamess/libcchem/lib -lcchem -lrysq -L/usr/local/cuda/lib64 -lcudart -lcublas -lcublas_device -lcudadevrt -L/usr/local/gamess-cuda-lib/boost_1_72_0/lib -lboost_thread -lboost_system -L/usr/local/gamess-cuda-lib/hdf5/lib64 -lhdf5 -lz -lstdc++ -lgomp -lpthread -ldl -L/usr/local/gamess-cuda-lib/libint/lib/ -lint2 prec.o params.o mpqcst.o -L/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core -L/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core ga.o zga.o -lga -larmci -L/usr/local/gamess-cuda-lib/ga/lib -L/usr/local/openmpi/lib -lmpi -lmpi_mpifh
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: ga.o: in function ddi_pbeg_': /usr/local/gamess/object/ga.F:400: undefined reference togamess_mpiinit'
collect2: error: ld returned 1 exit status
set rc=1
unset echo
Unfortunately, there was an error while linking GAMESS. 3.828u 0.429s 0:04.27 99.2% 0+0k 0+926384io 0pf+0w make: *** [/usr/local/gamess/Makefile.in:73: /usr/local/gamess/gamess.00.x] Error 1
acandac
commented
4 years ago Oh, by the way! I use openmpi libraries for parallel implimentation of libcchem. I noticed that you use intelMPI libraries. Would that be the cause of the installation problem? it appears that ga does not seem to be compatible with gamess_mpiinit !??
Regards,
acandac
commented
4 years ago One more thing I noticed! My previously installed gamess.00.x is gone now. I guess make removed gamess.00.x and tried to relink gamess.00.x after make..
colleeneb
commented
4 years ago At least there are less errors now! ;) I think it should work with OpenMPI, too.
/usr/local/gamess/object/ga.F:400: undefined reference to gamess_mpiinit'
This error usually means that ga.F calls gamess_mpi_init_, but no other object file or library in the link line is providing a definition for it.
It appears to be defined in zga.c
$ grep -r gamess_mpi_init source/*
source/ga.src: call gamess_mpi_init()
source/zga.c:void gamess_mpi_init_() {Could you check that zga.o is in the objects/ directory and run nm on it like below:
$ nm object/zga.o
0000000000000000 T gamess_mpi_init_
U MPI_Init_threadIt does look like it's being pulled into the linking phase, based on your output.
One more thing I noticed! My previously installed gamess.00.x is gone now. I guess make removed gamess.00.x and tried to relink gamess.00.x after make..
ah, right-- if when you ran ./config the second time (for libcchem), you gave it the same version as before, I think it overwrites it. (I'd have to try to be sure). So next time, we can give a different version to ./config
davpoolechem
commented
4 years ago Hi,
The missing definition comes from source/zga.src, which defines gamess_mpi_init under the condition that the MPI environment variable is defined. Try recompiling zga.src with the command "$CCOMP -DMPI -I/path/to/MPI/include -o object/zga.o source/zga.c", where $CCOMP is the C compiler you wish to use.
OpenMPI should work fine with GAMESS, including GAMESS+LibCChem.
The removal of gamess.00.x comes with the use of the "make clean" command iirc.
acandac
commented
4 years ago Hi all!
"Could you check that zga.o is in the objects/ directory and run nm on it like below: $ nm object/zga.o 0000000000000000 T gamess_mpiinit U MPI_Init_thread "
Yes, object/zga.o is available. However, runing nm on it gives out nothing ! (Previously, as suggested, I had generated zga.o by gcc -c zga.c in source directory then moved zga.o to ../object)
"Try recompiling zga.src with the command "$CCOMP -DMPI -I/path/to/MPI/include -o object/zga.o source/zga.c", where $CCOMP is the C compiler you wish to use." I tried to recompile zga.src as follows but I got the following error message. Hope I am not doing something wrong here! I will appreciate your further guidance on this issue. best,
gcc -DMPI -I/usr/local/openmpi/include -o object/zga.o source/zga.c
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crt1.o: in function _start': /home/abuild/rpmbuild/BUILD/glibc-2.26/csu/../sysdeps/x86_64/start.S:110: undefined reference tomain'
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: /tmp/ccwWlbjN.o: in function gamess_mpi_init_': zga.c:(.text+0x27): undefined reference toMPI_Init_thread'
collect2: error: ld returned 1 exit status
acandac
commented
4 years ago Here is what I have in zga.c
/ ----- this sets up running GA over MPI: used only with LIBCCHEM ----- /
void gamess_mpiinit() { int provided; int argc = 0; char **argv; MPI_Init_thread(&argc, &argv, MPI_THREAD_MULTIPLE, &provided); // printf("MPI_Init_thread returned %i\n", provided); }
colleeneb
commented
4 years ago could you try:
$ rm object/zga.o
$ make? I'll try to reproduce in a bit
colleeneb
commented
4 years ago this is what I get:
$ rm object/zga.o
$ make
gcc -c -DLINUX64 -m64 -o /home/bertoni/development/gamess/object/zunix.o /home/bertoni/development/gamess/source/zunix.c
unset echo
gcc -c -DLINUX64 -m64 -DMPI -I/soft/compilers/intel-2018/compilers_and_libraries_2018.1.163/linux/mpi/intel64/include -o object/zga.o source/zga.c
unset echo
Mon Mar 9 20:10:07 UTC 2020
GAMESS will be linked into the binary file gamess.00.cchem.x.
The name of the linker on this machine is gfortran,
and the linker options are " ".
Object code list begins "gamess.o unport.o",
followed by BLAS object code " ",
followed by LAPACK object code "dgeev.o dgesvd.o zheev.o",
followed by VECTOR object code " ",
followed by memory object code "zunix.o",
followed by the standard GAMESS object code list,
aldeci.o algnci.o basccn.o basecp.o basext.o basg3l.o bashuz.o bashz2.o baskar.o basminix.o basn21.o basn31.o baspcn.o basg3x.o bassto.o casino.o ccaux.o ccddi.o ccqaux.o ccquad.o ccsdt.o ceeis.o cepa.o cn\
glob.o chgpen.o cimf.o ciminf.o cimi.o cimlib.o cimsub.o cisgrd.o comp.o cosmo.o cosprt.o cphf.o cpmchf.o cprohf.o cpuhf.o dccc.o dcgrd.o dcgues.o dcint2.o dclib.o dcmp2.o dcscf.o dctran.o ddilib.o delocl.\
o demrpt.o dft.o dftaux.o dftbfo.o dftbgr.o dftbhs.o dftblb.o dftbsk.o dftbtd.o dftbx.o dftdis.o dftfun.o dftgrd.o dftint.o dftxca.o dftxcb.o dftxcc.o dftxcd.o dftxce.o dftxcf.o dftxcg.o diab.o dmulti.o dr\
c.o eaipcc.o ecp.o ecpder.o ecplib.o ecppot.o efpmodule.o efchtr.o efdrvr.o efelec.o efgrd2.o efgrda.o efgrdb.o efgrdc.o efinp.o efinta.o efintb.o efmo.o efmograd.o efmograd_es.o efmograd_exrep.o efmograd_\
disp.o efmograd_pol.o efpaul.o efpcm.o efpcov.o efpfmo.o eftei.o eigen.o elglib.o elgloc.o elgscf.o eomcc.o ewald.o excorr.o ffield.o fmo.o fmoafo.o fmocp.o fmoesd.o fmogrd.o fmoh1a.o fmoh2a.o fmoh2b.o fmo\
h2c.o fmohss.o fmoint.o fmoio.o fmoio_read.o fmolib.o fmomm.o fmopbc.o fmoprp.o
frfmt.o fsodci.o g3.o globop.o gmcpt.o gradex.o guess.o grd1.o grd2a.o grd2b.o grd2c.o gugdga.o gugdgb.o gugdm.o gugdm2.o gugdrt.o gugem.o gugsrt.o gvb.o hess.o hss1a.o hss1b.o hss1c.o hss2a.o hss2b.o hss2\
c.o inputa.o inputb.o inputc.o int1.o int2a.o int2b.o int2c.o int2d.o int2f.o int2g.o int2r.o int2s.o iolib.o ivocas.o lagran.o local.o locatd.o loccd.o locpol.o locsvd.o lrd.o lut.o modmcpdft.o mcpdft.o m\
cpgrd.o mcpinp.o mcpint.o mcpl10.o mcpl20.o mcpl30.o mcpl40.o mcpl50.o mcpl60.o mcpl70.o mcpl80.o mccas.o mcjac.o mcqdpt.o mcqdwt.o mcqud.o mcscf.o mctwo.o mdefp.o mexing.o mltfmo.o mm23.o modmnfun.o morok\
m.o mnsol.o mp2.o mp2ddi.o mp2grd.o mp2gr2.o mp2ims.o mpcdat.o mpcdatpm6.o mpcgrd.o mpchbond.o mpcint.o mpcmol.o mpcmsc.o mpcpcm.o mthlib.o nameio.o nebpath.o nmr.o
optcix.o ordint.o ormas1.o ormpt2.o parley.o pcm.o pcmcav.o pcmcv2.o pcmder.o pcmdis.o pcmhss.o pcmief.o pcmpol.o pcmvch.o prpamm.o prpel.o prplib.o prppop.o qeigen.o qfmm.o qmfm.o qrel.o quanpo.o raman.o \
reorg.o rhfuhf.o ricab.o riint.o rimp2.o rimp2omp.o rimp2grd.o rmd.o rmddat.o rmdgen.o rmdwrk.o rmdrun.o roeom.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.o secor.o sfdft.o sfgrad.o sobrt.o soffac.o\
solib.o sozeff.o statpt.o hrmrst.o surf.o svpchg.o svpinp.o svpleb.o symhi.o symorb.o symslc.o tddft.o tddefp.o tddfun.o tddfxc.o tddgrd.o tddint.o tddnlr.o tddxca.o tddxcc.o tddxcd_m05.o tddxcd_m06.o tdd\
xcd_m08.o tddxcd_pkzb.o tddxcd_revtpss.o tddxcd_tpss.o tddxcd_vs98.o tddxce.o tdhf.o tdx.o tdxio.o tdxitr.o tdxni.o tdxprp.o trans.o trfdm2.o trnstn.o trudge.o umpddi.o utddft.o utdgrd.o vibanl.o vscf.o vv\
os.o zapddi.o zmatrx.o mod_nosp_basis.o mod_grid_storage.o mod_dft_partfunc.o mod_dft_molgrid.o mod_dft_fuzzycell.o mod_dft_gridint.o
stubcc3.o
prec.o params.o
Choices for some optional plug-in codes are
Tinker/SIMOMM code skipped, using dummy file qmmm.o
Both VB programs skipped, using dummy file vbdum.o
Nuclear Electron Orbital code skipped, using dummy file neostb.o
Using LIBCCHEM add-in C++ code for CPUs and/or Nvidia/CUDA GPUs.
LIBCCHEM's libraries are
cchem.o -L/home/bertoni/development/gamess/libcchem/lib -lcchem -lrysq -L/soft/compilers/cuda/cuda-10.0.130//lib64 -lcudart -lcublas -lcudadevrt -L/home/bertoni/opt/boost//lib -lboost_thread -lboost_syste\
m -L/home/bertoni/opt/hdf5//lib -lhdf5 -lz -lstdc++ -lgomp -lpthread -ldl
Natural Bond Orbital (NBO) code skipped, using dummy file nbostb.o
MPQC code skipped, using dummy file mpqcst.o
The message passing libraries searched are
ga.o zga.o -lga -larmci -L/home/bertoni/gpu_tests/cp11/gamess/libcchem/externals/ga//lib -L/soft/compilers/intel-2018/compilers_and_libraries_2018.1.163/linux/mpi/lib64 -lmpi -lmpigf -lmpigi -lrt
Other libraries, including math libraries, to be searched are
-L/soft/compilers/intel-2019/compilers_and_libraries/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core
Linker messages (if any) follow...
dgeev.o dgesvd.o zheev.o
gfortran -L/home/bertoni/development/gamess/libcchem/boost/lib -o /home/bertoni/development/gamess/gamess.00.cchem.x -I/home/bertoni/development/gamess/object gamess.o unport.o dgeev.o dgesvd.o zheev.o zun\
ix.o aldeci.o algnci.o basccn.o basecp.o basext.o basg3l.o bashuz.o bashz2.o baskar.o basminix.o basn21.o basn31.o baspcn.o basg3x.o bassto.o casino.o ccaux.o ccddi.o ccqaux.o ccquad.o ccsdt.o ceeis.o cepa\
.o cnglob.o chgpen.o cimf.o ciminf.o cimi.o cimlib.o cimsub.o cisgrd.o comp.o cosmo.o cosprt.o cphf.o cpmchf.o cprohf.o cpuhf.o dccc.o dcgrd.o dcgues.o dcint2.o dclib.o dcmp2.o dcscf.o dctran.o ddilib.o de\
locl.o demrpt.o dft.o dftaux.o dftbfo.o dftbgr.o dftbhs.o dftblb.o dftbsk.o dftbtd.o dftbx.o dftdis.o dftfun.o dftgrd.o dftint.o dftxca.o dftxcb.o dftxcc.o dftxcd.o dftxce.o dftxcf.o dftxcg.o diab.o dmulti\
.o drc.o eaipcc.o ecp.o ecpder.o ecplib.o ecppot.o efpmodule.o efchtr.o efdrvr.o efelec.o efgrd2.o efgrda.o efgrdb.o efgrdc.o efinp.o efinta.o efintb.o efmo.o efmograd.o efmograd_es.o efmograd_exrep.o efmo\
grad_disp.o efmograd_pol.o efpaul.o efpcm.o efpcov.o efpfmo.o eftei.o eigen.o elglib.o elgloc.o elgscf.o eomcc.o ewald.o excorr.o ffield.o fmo.o fmoafo.o fmocp.o fmoesd.o fmogrd.o fmoh1a.o fmoh2a.o fmoh2b.\
o fmoh2c.o fmohss.o fmoint.o fmoio.o fmoio_read.o fmolib.o fmomm.o fmopbc.o fmoprp.o frfmt.o fsodci.o g3.o globop.o gmcpt.o gradex.o guess.o grd1.o grd2a.o grd2b.o grd2c.o gugdga.o gugdgb.o gugdm.o gugdm2.\
o gugdrt.o gugem.o gugsrt.o gvb.o hess.o hss1a.o hss1b.o hss1c.o hss2a.o hss2b.o hss2c.o inputa.o inputb.o inputc.o int1.o int2a.o int2b.o int2c.o int2d.o int2f.o int2g.o int2r.o int2s.o iolib.o ivocas.o l\
agran.o local.o locatd.o loccd.o locpol.o locsvd.o lrd.o lut.o modmcpdft.o mcpdft.o mcpgrd.o mcpinp.o mcpint.o mcpl10.o mcpl20.o mcpl30.o mcpl40.o mcpl50.o mcpl60.o mcpl70.o mcpl80.o mccas.o mcjac.o mcqdpt\
.o mcqdwt.o mcqud.o mcscf.o mctwo.o mdefp.o mexing.o mltfmo.o mm23.o modmnfun.o morokm.o mnsol.o mp2.o mp2ddi.o mp2grd.o mp2gr2.o mp2ims.o mpcdat.o mpcdatpm6.o mpcgrd.o mpchbond.o mpcint.o mpcmol.o mpcmsc.\
o mpcpcm.o mthlib.o nameio.o nebpath.o nmr.o optcix.o ordint.o ormas1.o ormpt2.o parley.o pcm.o pcmcav.o pcmcv2.o pcmder.o pcmdis.o pcmhss.o pcmief.o pcmpol.o pcmvch.o prpamm.o prpel.o prplib.o prppop.o qe\
igen.o qfmm.o qmfm.o qrel.o quanpo.o raman.o reorg.o rhfuhf.o ricab.o riint.o rimp2.o rimp2omp.o rimp2grd.o rmd.o rmddat.o rmdgen.o rmdwrk.o rmdrun.o roeom.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scr\
f.o secor.o sfdft.o sfgrad.o sobrt.o soffac.o solib.o sozeff.o statpt.o hrmrst.o surf.o svpchg.o svpinp.o svpleb.o symhi.o symorb.o symslc.o tddft.o tddefp.o tddfun.o tddfxc.o tddgrd.o tddint.o tddnlr.o td\
dxca.o tddxcc.o tddxcd_m05.o tddxcd_m06.o tddxcd_m08.o tddxcd_pkzb.o tddxcd_revtpss.o tddxcd_tpss.o tddxcd_vs98.o tddxce.o tdhf.o tdx.o tdxio.o tdxitr.o tdxni.o tdxprp.o trans.o trfdm2.o trnstn.o trudge.o \
umpddi.o utddft.o utdgrd.o vibanl.o vscf.o vvos.o zapddi.o zmatrx.o mod_nosp_basis.o mod_grid_storage.o mod_dft_partfunc.o mod_dft_molgrid.o mod_dft_fuzzycell.o mod_dft_gridint.o stubcc3.o qmmm.o vbdum.o n\
eostb.o nbostb.o cchem.o -L/home/bertoni/development/gamess/libcchem/lib -lcchem -lrysq -L/soft/compilers/cuda/cuda-10.0.130//lib64 -lcudart -lcublas -lcudadevrt -L/home/bertoni/opt/boost//lib -lboost_thre\
ad -lboost_system -L/home/bertoni/opt/hdf5//lib -lhdf5 -lz -lstdc++ -lgomp -lpthread -ldl prec.o params.o mpqcst.o -L/soft/compilers/intel-2019/compilers_and_libraries/linux/mkl/lib/intel64 -lmkl_gf_ilp64 \
-lmkl_gnu_thread -lmkl_core -L/soft/compilers/intel-2019/compilers_and_libraries/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core ga.o zga.o -lga -larmci -L/home/bertoni/gpu_tests/cp11/game\
ss/libcchem/externals/ga//lib -L/soft/compilers/intel-2018/compilers_and_libraries_2018.1.163/linux/mpi/lib64 -lmpi -lmpigf -lmpigi -lrt
set rc=0
unset echo
The linking of GAMESS to binary gamess.00.cchem.x was successful.
3.273u 0.841s 0:06.24 65.8% 0+0k 284616+378312io 0pf+0wHere is the result of make .
make gfortran -c -fdefault-integer-8 -g -ffpe-trap=invalid,zero,overflow -O2 -DHAVE_CCHEM -DBUILD_HF -DBUILD_MP2 -DBUILD_RI -DBUILD_CC -w -fno-aggressive-loop-optimizations -funconstrained-commons cchem.F unset echo gfortran -c -fdefault-integer-8 -g -ffpe-trap=invalid,zero,overflow -O2 -std=legacy -I/usr/local/gamess-cuda-lib/ga/include -w -fno-aggressive-loop-optimizations -funconstrained-commons ga.F unset echo gcc -c -DLINUX64 -m64 -o /usr/local/gamess/object/zunix.o /usr/local/gamess/source/zunix.c unset echo gcc -c -DLINUX64 -m64 -DMPI -I/usr/local/openmpi/include -o object/zga.o source/zga.c unset echo Mon Mar 9 23:01:42 +03 2020 GAMESS will be linked into the binary file gamess.00.x.
The name of the linker on this machine is gfortran, and the linker options are " ".
Object code list begins "gamess.o unport.o", followed by BLAS object code " ", followed by LAPACK object code "dgeev.o dgesvd.o zheev.o", followed by VECTOR object code " ", followed by memory object code "zunix.o", followed by the standard GAMESS object code list,
aldeci.o algnci.o basccn.o basecp.o basext.o basg3l.o bashuz.o bashz2.o baskar.o basminix.o basn21.o basn31.o baspcn.o basg3x.o bassto.o casino.o ccaux.o ccddi.o ccqaux.o ccquad.o ccsdt.o ceeis.o cepa.o cnglob.o chgpen.o cimf.o ciminf.o cimi.o cimlib.o cimsub.o cisgrd.o comp.o cosmo.o cosprt.o cphf.o cpmchf.o cprohf.o cpuhf.o dccc.o dcgrd.o dcgues.o dcint2.o dclib.o dcmp2.o dcscf.o dctran.o ddilib.o delocl.o demrpt.o dft.o dftaux.o dftbfo.o dftbgr.o dftbhs.o dftblb.o dftbsk.o dftbtd.o dftbx.o dftdis.o dftfun.o dftgrd.o dftint.o dftxca.o dftxcb.o dftxcc.o dftxcd.o dftxce.o dftxcf.o dftxcg.o diab.o dmulti.o drc.o eaipcc.o ecp.o ecpder.o ecplib.o ecppot.o efpmodule.o efchtr.o efdrvr.o efelec.o efgrd2.o efgrda.o efgrdb.o efgrdc.o efinp.o efinta.o efintb.o efmo.o efmograd.o efmograd_es.o efmograd_exrep.o efmograd_disp.o efmograd_pol.o efpaul.o efpcm.o efpcov.o efpfmo.o eftei.o eigen.o elglib.o elgloc.o elgscf.o eomcc.o ewald.o excorr.o ffield.o fmo.o fmoafo.o fmocp.o fmoesd.o fmogrd.o fmoh1a.o fmoh2a.o fmoh2b.o fmoh2c.o fmohss.o fmoint.o fmoio.o fmoio_read.o fmolib.o fmomm.o fmopbc.o fmoprp.o frfmt.o fsodci.o g3.o globop.o gmcpt.o gradex.o guess.o grd1.o grd2a.o grd2b.o grd2c.o gugdga.o gugdgb.o gugdm.o gugdm2.o gugdrt.o gugem.o gugsrt.o gvb.o hess.o hss1a.o hss1b.o hss1c.o hss2a.o hss2b.o hss2c.o inputa.o inputb.o inputc.o int1.o int2a.o int2b.o int2c.o int2d.o int2f.o int2g.o int2r.o int2s.o iolib.o ivocas.o lagran.o local.o locatd.o loccd.o locpol.o locsvd.o lrd.o lut.o modmcpdft.o mcpdft.o mcpgrd.o mcpinp.o mcpint.o mcpl10.o mcpl20.o mcpl30.o mcpl40.o mcpl50.o mcpl60.o mcpl70.o mcpl80.o mccas.o mcjac.o mcqdpt.o mcqdwt.o mcqud.o mcscf.o mctwo.o mdefp.o mexing.o mltfmo.o mm23.o modmnfun.o morokm.o mnsol.o mp2.o mp2ddi.o mp2grd.o mp2gr2.o mp2ims.o mpcdat.o mpcdatpm6.o mpcgrd.o mpchbond.o mpcint.o mpcmol.o mpcmsc.o mpcpcm.o mthlib.o nameio.o nebpath.o nmr.o optcix.o ordint.o ormas1.o ormpt2.o parley.o pcm.o pcmcav.o pcmcv2.o pcmder.o pcmdis.o pcmhss.o pcmief.o pcmpol.o pcmvch.o prpamm.o prpel.o prplib.o prppop.o qeigen.o qfmm.o qmfm.o qrel.o quanpo.o raman.o reorg.o rhfuhf.o ricab.o riint.o rimp2.o rimp2omp.o rimp2grd.o rmd.o rmddat.o rmdgen.o rmdwrk.o rmdrun.o roeom.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.o secor.o sfdft.o sfgrad.o sobrt.o soffac.o solib.o sozeff.o statpt.o hrmrst.o surf.o svpchg.o svpinp.o svpleb.o symhi.o symorb.o symslc.o tddft.o tddefp.o tddfun.o tddfxc.o tddgrd.o tddint.o tddnlr.o tddxca.o tddxcc.o tddxcd_m05.o tddxcd_m06.o tddxcd_m08.o tddxcd_pkzb.o tddxcd_revtpss.o tddxcd_tpss.o tddxcd_vs98.o tddxce.o tdhf.o tdx.o tdxio.o tdxitr.o tdxni.o tdxprp.o trans.o trfdm2.o trnstn.o trudge.o umpddi.o utddft.o utdgrd.o vibanl.o vscf.o vvos.o zapddi.o zmatrx.o mod_nosp_basis.o mod_grid_storage.o mod_dft_partfunc.o mod_dft_molgrid.o mod_dft_fuzzycell.o mod_dft_gridint.o stubcc3.o prec.o params.o
Choices for some optional plug-in codes are Tinker/SIMOMM code skipped, using dummy file qmmm.o Both VB programs skipped, using dummy file vbdum.o Nuclear Electron Orbital code skipped, using dummy file neostb.o Using LIBCCHEM add-in C++ code for CPUs and/or Nvidia/CUDA GPUs. LIBCCHEM's libraries are cchem.o -L/usr/local/gamess/libcchem/lib -lcchem -lrysq -L/usr/local/cuda/lib64 -lcudart -lcublas -lcublas_device -lcudadevrt -L/usr/local/gamess-cuda-lib/boost_1_72_0/lib -lboost_thread -lboost_system -L/usr/local/gamess-cuda-lib/hdf5/lib64 -lhdf5 -lz -lstdc++ -lgomp -lpthread -ldl -L/usr/local/gamess-cuda-lib/libint/lib/ -lint2 Natural Bond Orbital (NBO) code skipped, using dummy file nbostb.o MPQC code skipped, using dummy file mpqcst.o
The message passing libraries searched are ga.o zga.o -lga -larmci -L/usr/local/gamess-cuda-lib/ga/lib -L/usr/local/openmpi/lib -lmpi -lmpi_mpifh
Other libraries, including math libraries, to be searched are -L/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core
Linker messages (if any) follow... dgeev.o dgesvd.o zheev.o gfortran -L/usr/local/gamess/libcchem/boost/lib -o /usr/local/gamess/gamess.00.x -I/usr/local/gamess/object gamess.o unport.o dgeev.o dgesvd.o zheev.o zunix.o aldeci.o algnci.o basccn.o basecp.o basext.o basg3l.o bashuz.o bashz2.o baskar.o basminix.o basn21.o basn31.o baspcn.o basg3x.o bassto.o casino.o ccaux.o ccddi.o ccqaux.o ccquad.o ccsdt.o ceeis.o cepa.o cnglob.o chgpen.o cimf.o ciminf.o cimi.o cimlib.o cimsub.o cisgrd.o comp.o cosmo.o cosprt.o cphf.o cpmchf.o cprohf.o cpuhf.o dccc.o dcgrd.o dcgues.o dcint2.o dclib.o dcmp2.o dcscf.o dctran.o ddilib.o delocl.o demrpt.o dft.o dftaux.o dftbfo.o dftbgr.o dftbhs.o dftblb.o dftbsk.o dftbtd.o dftbx.o dftdis.o dftfun.o dftgrd.o dftint.o dftxca.o dftxcb.o dftxcc.o dftxcd.o dftxce.o dftxcf.o dftxcg.o diab.o dmulti.o drc.o eaipcc.o ecp.o ecpder.o ecplib.o ecppot.o efpmodule.o efchtr.o efdrvr.o efelec.o efgrd2.o efgrda.o efgrdb.o efgrdc.o efinp.o efinta.o efintb.o efmo.o efmograd.o efmograd_es.o efmograd_exrep.o efmograd_disp.o efmograd_pol.o efpaul.o efpcm.o efpcov.o efpfmo.o eftei.o eigen.o elglib.o elgloc.o elgscf.o eomcc.o ewald.o excorr.o ffield.o fmo.o fmoafo.o fmocp.o fmoesd.o fmogrd.o fmoh1a.o fmoh2a.o fmoh2b.o fmoh2c.o fmohss.o fmoint.o fmoio.o fmoio_read.o fmolib.o fmomm.o fmopbc.o fmoprp.o frfmt.o fsodci.o g3.o globop.o gmcpt.o gradex.o guess.o grd1.o grd2a.o grd2b.o grd2c.o gugdga.o gugdgb.o gugdm.o gugdm2.o gugdrt.o gugem.o gugsrt.o gvb.o hess.o hss1a.o hss1b.o hss1c.o hss2a.o hss2b.o hss2c.o inputa.o inputb.o inputc.o int1.o int2a.o int2b.o int2c.o int2d.o int2f.o int2g.o int2r.o int2s.o iolib.o ivocas.o lagran.o local.o locatd.o loccd.o locpol.o locsvd.o lrd.o lut.o modmcpdft.o mcpdft.o mcpgrd.o mcpinp.o mcpint.o mcpl10.o mcpl20.o mcpl30.o mcpl40.o mcpl50.o mcpl60.o mcpl70.o mcpl80.o mccas.o mcjac.o mcqdpt.o mcqdwt.o mcqud.o mcscf.o mctwo.o mdefp.o mexing.o mltfmo.o mm23.o modmnfun.o morokm.o mnsol.o mp2.o mp2ddi.o mp2grd.o mp2gr2.o mp2ims.o mpcdat.o mpcdatpm6.o mpcgrd.o mpchbond.o mpcint.o mpcmol.o mpcmsc.o mpcpcm.o mthlib.o nameio.o nebpath.o nmr.o optcix.o ordint.o ormas1.o ormpt2.o parley.o pcm.o pcmcav.o pcmcv2.o pcmder.o pcmdis.o pcmhss.o pcmief.o pcmpol.o pcmvch.o prpamm.o prpel.o prplib.o prppop.o qeigen.o qfmm.o qmfm.o qrel.o quanpo.o raman.o reorg.o rhfuhf.o ricab.o riint.o rimp2.o rimp2omp.o rimp2grd.o rmd.o rmddat.o rmdgen.o rmdwrk.o rmdrun.o roeom.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.o secor.o sfdft.o sfgrad.o sobrt.o soffac.o solib.o sozeff.o statpt.o hrmrst.o surf.o svpchg.o svpinp.o svpleb.o symhi.o symorb.o symslc.o tddft.o tddefp.o tddfun.o tddfxc.o tddgrd.o tddint.o tddnlr.o tddxca.o tddxcc.o tddxcd_m05.o tddxcd_m06.o tddxcd_m08.o tddxcd_pkzb.o tddxcd_revtpss.o tddxcd_tpss.o tddxcd_vs98.o tddxce.o tdhf.o tdx.o tdxio.o tdxitr.o tdxni.o tdxprp.o trans.o trfdm2.o trnstn.o trudge.o umpddi.o utddft.o utdgrd.o vibanl.o vscf.o vvos.o zapddi.o zmatrx.o mod_nosp_basis.o mod_grid_storage.o mod_dft_partfunc.o mod_dft_molgrid.o mod_dft_fuzzycell.o mod_dft_gridint.o stubcc3.o qmmm.o vbdum.o neostb.o nbostb.o cchem.o -L/usr/local/gamess/libcchem/lib -lcchem -lrysq -L/usr/local/cuda/lib64 -lcudart -lcublas -lcublas_device -lcudadevrt -L/usr/local/gamess-cuda-lib/boost_1_72_0/lib -lboost_thread -lboost_system -L/usr/local/gamess-cuda-lib/hdf5/lib64 -lhdf5 -lz -lstdc++ -lgomp -lpthread -ldl -L/usr/local/gamess-cuda-lib/libint/lib/ -lint2 prec.o params.o mpqcst.o -L/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core -L/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core ga.o zga.o -lga -larmci -L/usr/local/gamess-cuda-lib/ga/lib -L/usr/local/openmpi/lib -lmpi -lmpi_mpifh set rc=0 unset echo
The linking of GAMESS to binary gamess.00.x was successful. 4.202u 0.485s 0:04.69 99.7% 0+0k 0+925936io 0pf+0w
colleeneb
commented
4 years ago It looks successful, no?
acandac
commented
4 years ago Before executing make , a couple of hours a go , I reconfigured and reinstalled gamess.00.x (the sockets version with no libcchem) , and then reconfigured gamess with libcchem.
acandac
commented
4 years ago yes looks like that! My question is that why the linked binary gamess.00.x is not named gamess.00.cchem.x ?
acandac
commented
4 years ago I previously backed up the sockets version of gamess as gamess.00.x.backup I see that the newly generated gamess.00.x differs in size from gamess.00.x.backup
-rwxr-xr-x 1 root 504 266750192 Mar 9 23:01 gamess.00.x -rwxr-xr-x 1 root 504 105843008 Mar 9 21:44 gamess.00.x.backup
acandac
commented
4 years ago Would it be OK if I renamed gamess.00.x as gamess.00.cchem.x ?
colleeneb
commented
4 years ago Would it be OK if I renamed gamess.00.x as gamess.00.cchem.x ?
Yeah, this is totally fine.
The more "standard" way to do it is to use different answers to the prompt:
"Please provide a version number for the GAMESS executable."
"This will be used as the middle part of the binary's name,"
"for example: gamess.00.x"
"Version? [00] "when you rerun ./config after compiling libcchem.
So the first non-libcchem time I compile gamess, I just use "00", which produces gamess.00.x. The second time, after compiling libcchem with cmake, I use "00.cchem", which produces gamess.00.cchem.x
does this make sense?
Or, if you want, you can change the name in Makefile, too.
acandac
commented
4 years ago YES, IT DOES :) Thank you all for helping me out with the installation of LIBCCHEM.. It is now time I tested gamess.00.cchem.x
I am now modifying rungms. I see in rungms that no lines is available for openmpi . So , I'll have to add the necessary lines for openmpi myself manually.
I opted ga for TARGET in rungms.
I added the following lines in ga) section :
if ($GA_MPI_CHOICE == openmpi) then set GA_MPI_ROOT=/usr/local/openmpi endif
if ($GA_MPI_CHOICE == openmpi) set MPI_KICKOFF_STYLE=hydra
if ($GA_MPI_CHOICE == openmpi) set path=($GA_MPI_ROOT/bin $path)
setenv LD_LIBRARY_PATH /usr/local/cuda/lib64:$LD_LIBRARY_PATH
if ($GA_MPI_CHOICE == openmpi) then setenv LD_LIBRARY_PATH $GA_MPI_ROOT/lib:$LD_LIBRARY_PATH endif
setenv LD_LIBRARY_PATH /opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64:$LD_LIBRARY_PATH
setenv GMS_CCHEM '1'
setenv CCHEM 'devices=;memory=6g' #
Is there anything else I should add or make addition in rungms files ?
Regards,
acandac
commented
4 years ago Alternatively, if you have a rungms file that includes openmpi information, could you please email it to me at cenk_andac@yahoo.com.
Regards,
colleeneb
commented
4 years ago What you have seems reasonable, but I don't have time to reproduce right away. FWIW, normally I run with rungms-dev, and it looks like it has openmpi support. For example:
./rungms-dev rhf.inp 00 1 1It should call the GPU code if the name of the gamess executable is gamess.cchem.00.x (this is hard-coded in rungms-dev, maybe we should change it). I just copied my gamess.00.x with libcchem to gamess.cchem.00.x.
To test, you can copy a test code out of tests, like:
cp gamess.00.cchem.x gamess.cchem.00.x
cp tests/libcchem/ri/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.inp .
./rungms-dev imp2-ketamine.energy.6311Gdp_sph-cct_sph.inp 00 1 1Could you give this a try? My executable is crashing right now unfortunately, so I'm not sure if my setup is totally right (although it has worked successfully before, just need to debug a bit more.)
acandac
commented
4 years ago Hello, I have tried the command line in root. Here is the error message I got.
-----debug libcchem---- the execution path is /usr/local/openmpi/bin /root/bin /sbin /usr/sbin /usr/local/sbin /opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64 /opt/intel/compilers_and_libraries_2019.5.281/linux/bin /usr/local/amber18/bin /bin /usr/bin /usr/local/cuda/bin /usr/local/cuda/samples/bin/x86_64/linux/release /usr/local/openmpi/bin /usr/local/gdrcopy/bin /usr/local/gamess /usr/local/bin /usr/lib/mit/sbin the library path is /usr/local/gamess-cuda-lib/hdf5/lib:/usr/local/gamess-cuda-lib/boost_1_72_0/lib:/usr/local/openmpi/lib:/usr/local/cuda/lib64:/usr/local/cuda/lib:/usr/local/gamess/libcchem/lib:/opt/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2019.5.281/linux/tbb/lib/intel64_lin/gcc4.7:/opt/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin:/usr/local/amber18/lib::/usr/local/cuda/lib64:/usr/local/openmpi/lib64:/usr/local/gdrcopy/lib64 The dynamically linked libraries for this binary are /usr/local/gamess/gamess.cchem.00.x :
linux-vdso.so.1 (0x00007ffeb33f2000)
libcudart.so.9.2 => /usr/local/cuda/lib64/libcudart.so.9.2 (0x00007f96ac4ee000)
libcublas.so.9.2 => /usr/local/cuda/lib64/libcublas.so.9.2 (0x00007f96a8aa0000)
libboost_thread.so.1.72.0 => /usr/local/gamess-cuda-lib/boost_1_72_0/lib/libboost_thread.so.1.72.0 (0x00007f96a887c000)
libboost_system.so.1.72.0 => /usr/local/gamess-cuda-lib/boost_1_72_0/lib/libboost_system.so.1.72.0 (0x00007f96a867a000)
libhdf5.so.10 => not found
libz.so.1 => /lib64/libz.so.1 (0x00007f96a8463000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f96a80d9000)
libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x00007f96a7ea9000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f96a7c8b000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f96a7a87000)
libmkl_gf_ilp64.so => /opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_gf_ilp64.so (0x00007f96a6fcc000)
libmkl_gnu_thread.so => /opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so (0x00007f96a56f3000)
libmkl_core.so => /opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_core.so (0x00007f96a13c2000)
libmpi.so.40 => /usr/local/openmpi/lib/libmpi.so.40 (0x00007f96a10ab000)
libmpi_mpifh.so.40 => /usr/local/openmpi/lib/libmpi_mpifh.so.40 (0x00007f96a0e4a000)
libgfortran.so.4 => /usr/lib64/libgfortran.so.4 (0x00007f96a0a76000)
libm.so.6 => /lib64/libm.so.6 (0x00007f96a073e000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f96a0526000)
libquadmath.so.0 => /usr/lib64/libquadmath.so.0 (0x00007f96a02e6000)
libc.so.6 => /lib64/libc.so.6 (0x00007f969ff2c000)
librt.so.1 => /lib64/librt.so.1 (0x00007f969fd24000)
/lib64/ld-linux-x86-64.so.2 (0x00007f96ac758000)
libopen-rte.so.40 => /usr/local/openmpi/lib/libopen-rte.so.40 (0x00007f969fa6f000)
libopen-pal.so.40 => /usr/local/openmpi/lib/libopen-pal.so.40 (0x00007f969f75c000)
libudev.so.1 => /usr/lib64/libudev.so.1 (0x00007f969f539000)
libpciaccess.so.0 => /usr/lib64/libpciaccess.so.0 (0x00007f969f32f000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007f969f12c000)
libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f969ef15000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00007f969ecec000)
libcap.so.2 => /usr/lib64/libcap.so.2 (0x00007f969eae7000)
libpcre.so.1 => /usr/lib64/libpcre.so.1 (0x00007f969e85a000)orterun has detected an attempt to run as root.
Running as root is strongly discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state.
We strongly suggest that you run orterun as a non-root user.
unset echo ----- accounting info ----- Files used on the master node cadd0atjenk were: -rw-r--r-- 1 root 504 2515 Mar 10 13:52 /usr/local/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.F05 -rw-r--r-- 1 root 504 12 Mar 10 13:52 /usr/local/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.nodes.mpd Tue Mar 10 13:52:54 +03 2020 0.147u 0.019s 0:00.17 88.2% 0+0k 3160+144io 4pf+0w
acandac
commented
4 years ago I have also tried it in usr mode, but no luck either!
/usr/local/gamess/rungms-dev rimp2-ketamine.energy.6311Gdp_sph-cct_sph.inp 0 0 1 1 Please run 'config' first, to set up GAMESS compiling information
acandac
commented
4 years ago Although libhadf5.so.10 is in /usr/local/gamess-cuda-lib/hdf5/lib64 rungms-dev output says it can not find it. Somewhat hdf5 library is not set then. I try to set it on LD_LIBRARY_PATH
acandac
commented
4 years ago OK. This time rungms-dev found the hdf5 library, but gave the same running as root error.
linux-vdso.so.1 (0x00007ffcdcd95000)
libcudart.so.9.2 => /usr/local/cuda/lib64/libcudart.so.9.2 (0x00007fa70e5b0000)
libcublas.so.9.2 => /usr/local/cuda/lib64/libcublas.so.9.2 (0x00007fa70ab62000)
libboost_thread.so.1.72.0 => /usr/local/gamess-cuda-lib/boost_1_72_0/lib/libboost_thread.so.1.72.0 (0x00007fa70a93e000)
libboost_system.so.1.72.0 => /usr/local/gamess-cuda-lib/boost_1_72_0/lib/libboost_system.so.1.72.0 (0x00007fa70a73c000)
libhdf5.so.10 => /usr/local/gamess-cuda-lib/hdf5/lib64/libhdf5.so.10 (0x00007fa70a24a000)
libz.so.1 => /lib64/libz.so.1 (0x00007fa70a033000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fa709ca9000)
libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x00007fa709a79000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fa70985b000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fa709657000)
libmkl_gf_ilp64.so => /opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_gf_ilp64.so (0x00007fa708b9c000)
libmkl_gnu_thread.so => /opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so (0x00007fa7072c3000)
libmkl_core.so => /opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_core.so (0x00007fa702f92000)
libmpi.so.40 => /usr/local/openmpi/lib/libmpi.so.40 (0x00007fa702c7b000)
libmpi_mpifh.so.40 => /usr/local/openmpi/lib/libmpi_mpifh.so.40 (0x00007fa702a1a000)
libgfortran.so.4 => /usr/lib64/libgfortran.so.4 (0x00007fa702646000)
libm.so.6 => /lib64/libm.so.6 (0x00007fa70230e000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fa7020f6000)
libquadmath.so.0 => /usr/lib64/libquadmath.so.0 (0x00007fa701eb6000)
libc.so.6 => /lib64/libc.so.6 (0x00007fa701afc000)
librt.so.1 => /lib64/librt.so.1 (0x00007fa7018f4000)
/lib64/ld-linux-x86-64.so.2 (0x00007fa70e81a000)
libopen-rte.so.40 => /usr/local/openmpi/lib/libopen-rte.so.40 (0x00007fa70163f000)
libopen-pal.so.40 => /usr/local/openmpi/lib/libopen-pal.so.40 (0x00007fa70132c000)
libudev.so.1 => /usr/lib64/libudev.so.1 (0x00007fa701109000)
libpciaccess.so.0 => /usr/lib64/libpciaccess.so.0 (0x00007fa700eff000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007fa700cfc000)
libresolv.so.2 => /lib64/libresolv.so.2 (0x00007fa700ae5000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00007fa7008bc000)
libcap.so.2 => /usr/lib64/libcap.so.2 (0x00007fa7006b7000)
libpcre.so.1 => /usr/lib64/libpcre.so.1 (0x00007fa70042a000)orterun has detected an attempt to run as root.
Running as root is strongly discouraged as any mistake (e.g., in defining TMPDIR) or bug can result in catastrophic damage to the OS file system, leaving your system in an unusable state.
We strongly suggest that you run orterun as a non-root user.
unset echo ----- accounting info ----- Files used on the master node cadd0atjenk were: -rwxr-xr-x 1 root 504 2515 Mar 10 14:34 /usr/local/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.F05* -rw-r--r-- 1 root 504 12 Mar 10 14:34 /usr/local/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.nodes.mpd Tue Mar 10 14:34:25 +03 2020
acandac
commented
4 years ago OK , now I re-run rungms-dev as user in my home directory including all the required files : gamess.cchem.00.x, gamess.cchem.0.x gms-files.csh, install.info, rimp2-ketamine.energy.6311Gdp_sph-cct_sph.inp
Now I got the following error message asking for a mapper. which is probably not installed or configured somewhat.
Your job failed to map. Either no mapper was available, or none of the available mappers was able to perform the requested mapping operation. This can happen if you request a map type (e.g., loadbalance) and the corresponding mapper was not built.
Mapper result: mapped
unset echo ----- accounting info ----- Files used on the master node cadd0atjenk were: -rwxr-xr-x 1 jenk users 2515 Mar 10 14:47 /home/jenk/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.F05* -rw-r--r-- 1 jenk users 12 Mar 10 14:47 /home/jenk/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.nodes.mpd Tue Mar 10 14:47:14 +03 2020 0.171u 0.014s 0:00.18 100.0% 0+0k 0+120io 0pf+0w
acandac
commented
4 years ago Does this mean libcchem is working?
colleeneb
commented
4 years ago Not sure, but it's not good that you see the phrase "0 cores". make sure there's no space between the two 0s:
./rungms-dev ketamine.energy.6311Gdp_sph-cct_sph.inp 00 1 1
and like orterun says, don't run as root user, run in user-mode.
usually I run from the directory where ./rungms-dev is (usually ~/gamess/)
davpoolechem
commented
4 years ago Hi,
So it seems that LibCChem is being executed, i.e., GAMESS recognizes the existence of LibCChem and will eventually use it. However, it looked like the job failed to map because there were no processes that it could map, based on this statement: "Mapper result: mapped
This is reinforced when MPI kickoff says it is mapping 0 cores in 1 node.
I would try Colleen's recommendations on commands and see how that goes.
acandac
commented
4 years ago Hi!
"Not sure, but it's not good that you see the phrase "0 cores". make sure there's no space between the two 0s:
./rungms-dev ketamine.energy.6311Gdp_sph-cct_sph.inp 00 1 1
and like orterun says, don't run as root user, run in user-mode.
usually I run from the directory where ./rungms-dev is (usually ~/gamess/)"
This time I ran the gamess job as a user in ~/gamess directory.
./rungms-dev rimp2-ketamine.energy.6311Gdp_sph-cct_sph.inp 00 1 1
İt seemed working at the beginning, but it gave an error message at the end.
--------------------------
DF-RHF SCF CALCULATION
--------------------------
NUCLEAR ENERGY = 1301.6330629313
MAXIT = 30 NPUNCH= 2
EXTRAP=T DAMP=F SHIFT=F RSTRCT=F DIIS=F DEM=F SOSCF=T
DENSITY MATRIX CONV= 2.00E-06
SOSCF WILL OPTIMIZE 20727 ORBITAL ROTATIONS, SOGTOL= 0.250
MEMORY REQUIRED FOR RHF ITERS= 1405652 WORDS.DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 SCHWARZ INEQUALITY OVERHEAD: 74599 INTEGRALS, T= 0.02
NONZERO BLOCKSITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE ORB. GRAD INTEGRALS SKIPPED
spherical auxiliary basis set will be used to construct (L|M) 2231 cartesian auxiliary functions ---> 1817 spherical auxiliary functions
found 1 devices: each device will setup 1 cuda streams Device Number: 0 Device Name: GeForce GTX 1080 Ti CUDA runtime verison: 9.2 Free Memory (bytes): 11493965824
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 4 DUP FROM 0 with errorcode 8.
unset echo ----- accounting info ----- Files used on the master node cadd0atjenk were: -rwxr-xr-x 1 jenk users 2515 Mar 10 19:34 /home/jenk/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.F05* -rw-r--r-- 1 jenk users 36044800 Mar 10 19:34 /home/jenk/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.F10 -rw-r--r-- 1 jenk users 0 Mar 10 19:34 /home/jenk/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.F15 -rw-r--r-- 1 jenk users 12 Mar 10 19:34 /home/jenk/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.nodes.mpd Tue Mar 10 19:34:59 +03 2020 0.174u 0.039s 0:05.05 3.9% 0+0k 0+16520io 4pf+0w
acandac
commented
4 years ago Could this mean a memory problem?
Just in case here is my /proc/sys/kernel/shmmax value cat /proc/sys/kernel/shmmax 18446744073709551615
davpoolechem
commented
4 years ago Hi,
Based on the fact that it is an ARMCI error of sorts, it seems that this could be an issue with Global Arrays, or how LibCChem is interacting with it. Which version of Global Arrays are you using?
acandac
commented
4 years ago ga-5-1 I patched it first, and then configured it as follows
./configure --prefix=/usr/local/gamess/libcchem/ga --with-mpi-spawn CFLAGS= -g FFLAGS= -g
acandac
commented
4 years ago if I type make in libchem/externals/ga I see in config.log that make configures ga as follows ./configure --prefix=/usr/local/gamess/libcchem/externals/ga --with-sockets CFLAGS= -g FFLAGS= -g
acandac
commented
4 years ago So there is difference with flags --with-mpi-spawn and --with-sockets. Should I go with --with-sockets flag instead of --with-mpi-spawn?
davpoolechem
commented
4 years ago Hi,
You would want to use the --with-mpi-spawn flags rather than the --with-sockets flag.
The patched version of Global Arrays that can be used with LibCChem is more of a holdover from older versions of the code than anything else. I would recommend using a newer version of Global Arrays and linking to that, if you can.
acandac
commented
4 years ago Hi,
I installed ga-5-5 Then, reinstalled gamess as follows: cd /usr/local/gamess make clean make to test gamess installation in user mode cd /home/jenk/gamess rungms-dev rimp2-ketamine.energy.6311Gdp_sph-cct_sph.inp 00 1 1
DF-RHF SCF CALCULATION
--------------------------
NUCLEAR ENERGY = 1301.6330629313
MAXIT = 30 NPUNCH= 2
EXTRAP=T DAMP=F SHIFT=F RSTRCT=F DIIS=F DEM=F SOSCF=T
DENSITY MATRIX CONV= 2.00E-06
SOSCF WILL OPTIMIZE 20727 ORBITAL ROTATIONS, SOGTOL= 0.250
MEMORY REQUIRED FOR RHF ITERS= 1405652 WORDS.DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 SCHWARZ INEQUALITY OVERHEAD: 74599 INTEGRALS, T= 0.02
NONZERO BLOCKSITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE ORB. GRAD INTEGRALS SKIPPED
spherical auxiliary basis set will be used to construct (L|M) 2231 cartesian auxiliary functions ---> 1817 spherical auxiliary functions
found 1 devices: each device will setup 1 cuda streams Device Number: 0 Device Name: GeForce GTX 1080 Ti CUDA runtime verison: 9.2 Free Memory (bytes): 11493965824
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 4 DUP FROM 0 with errorcode 8.
unset echo ----- accounting info ----- Files used on the master node cadd0atjenk were: -rwxr-xr-x 1 jenk users 2515 Mar 12 01:30 /home/jenk/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.F05* -rw-r--r-- 1 jenk users 36044800 Mar 12 01:30 /home/jenk/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.F10 -rw-r--r-- 1 jenk users 0 Mar 12 01:30 /home/jenk/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.F15 -rw-r--r-- 1 jenk users 12 Mar 12 01:30 /home/jenk/gamess/scratch/rimp2-ketamine.energy.6311Gdp_sph-cct_sph.nodes.mpd Thu Mar 12 01:30:25 +03 2020 0.176u 0.041s 0:02.44 8.6% 0+0k 0+16456io 4pf+0w
acandac
commented
4 years ago I used the following command line to configure ga
./configure --prefix=/usr/local/gamess-cuda-lib/ga --with-mpi-spawn
Hi, I have a problem with installation of gamess libcchem. my OS is opensuse leap 15.0 gnu version : 7.4.1 math library : intel mkl coomunication library : openmpi
I installed boost_1_71_0 (as boost_1_46_1 that is included in the package does not install on my OS) After re-configuration of gamess for cuda and gpu installation (I have GTX1080ti GPU with pascal architechture) cd /usr/local/gamess/libcchem ./build-cchem >& build-cchem.log & Installation stops after a while. Installation output messages traces the error down to basis installation in cd /usr/local/gamess/libcchem/src/basis gamess@iastate.edu (My initial guess would be something related to the boost version I installed, boost_1_71_0)
I will appreciate it if you let me know a workaround to complete the installation
Thanks,
Here is the make error message :
In file included from /usr/include/c++/7/bits/stl_algobase.h:67:0, from /usr/include/c++/7/bits/char_traits.h:39, from /usr/include/c++/7/string:40, from /usr/include/c++/7/stdexcept:39, from /usr/include/c++/7/array:39, from /usr/include/c++/7/tuple:39, from /usr/include/c++/7/functional:54, from basis.cpp:1: /usr/include/c++/7/bits/stl_iterator.h:912:5: note: candidate: template<class _Iterator, class _Container> bool gnu_cxx::operator>(const __gnu_cxx::normal_iterator<_Iterator, _Container>&, const gnu_cxx::__normal_iterator<_Iterator, _Container>&) operator>(const normal_iterator<_Iterator, _Container>& lhs, ^
~~~ /usr/include/c++/7/bits/stl_iterator.h:912:5: note: template argument deduction/substitution failed: basis.cpp:114:41: note: ‘std::_Bind_helper<false, long int ()(const std::vector<const basis::shell_data>&, const basis::shell_data const&, const basis::shell_data const&), const boost::reference_wrapper<std::vector<const basis::shell_data, std::allocator<const basis::shell_data> > >, const boost::lambda::lambda_functor<boost::lambda::placeholder<1> >&, const boost::lambda::lambda_functor<boost::lambda::placeholder<2> >&>::type {aka std::_Bind<long int ((boost::reference_wrapper<std::vector<const basis::shell_data> >, boost::lambda::lambda_functor<boost::lambda::placeholder<1> >, boost::lambda::lambda_functor<boost::lambda::placeholder<2> >))(const std::vector<const basis::shell_data>&, const basis::shell_data const&, const basis::shell_data* const&)>}’ is not derived from ‘const __gnu_cxx::normal_iterator<_Iterator, _Container>’ boost::ref(shelldata), _1, _2) > 0); ^ In file included from /usr/include/c++/7/bits/stl_algobase.h:67:0, from /usr/include/c++/7/bits/char_traits.h:39, from /usr/include/c++/7/string:40, from /usr/include/c++/7/stdexcept:39, from /usr/include/c++/7/array:39, from /usr/include/c++/7/tuple:39, from /usr/include/c++/7/functional:54, from basis.cpp:1: /usr/include/c++/7/bits/stl_iterator.h:905:5: note: candidate: template<class _IteratorL, class _IteratorR, class _Container> bool gnu_cxx::operator>(const __gnu_cxx::normal_iterator<_IteratorL, _Container>&, const gnu_cxx::__normal_iterator<_IteratorR, _Container>&) operator>(const normal_iterator<_IteratorL, _Container>& lhs, ^~~~ /usr/include/c++/7/bits/stl_iterator.h:905:5: note: template argument deduction/substitution failed: basis.cpp:114:41: note: ‘std::_Bind_helper<false, long int ()(const std::vector<const basis::shell_data>&, const basis::shell_data const&, const basis::shell_data const&), const boost::reference_wrapper<std::vector<const basis::shell_data, std::allocator<const basis::shell_data> > >, const boost::lambda::lambda_functor<boost::lambda::placeholder<1> >&, const boost::lambda::lambda_functor<boost::lambda::placeholder<2> >&>::type {aka std::_Bind<long int ((boost::reference_wrapper<std::vector<const basis::shell_data> >, boost::lambda::lambda_functor<boost::lambda::placeholder<1> >, boost::lambda::lambda_functor<boost::lambda::placeholder<2> >))(const std::vector<const basis::shell_data>&, const basis::shell_data const&, const basis::shell_data* const&)>}’ is not derived from ‘const __gnu_cxx::normal_iterator<_IteratorL, _Container>’ boost::ref(shelldata), _1, _2) > 0); ^ make: *** [Makefile:308: basis.lo] Error 1