Thanks for your advice Christoph. Things have checked out. I ended up using the Docker container, and things seem to be going smoothly for now.
On Friday, February 18, 2022 at 12:05:06 PM UTC-5 Christoph Junghans wrote: > On Fri, Feb 18, 2022 at 09:25 Satyen Dhamankar <[email protected]> wrote: > >> Hi Christoph, thank you for your response! >> >> Unfortunately, it seems like there seems to be an issue with the spack >> installation itself. This is the error message I am seeing: (goto >> "========" to see error message) >> >> ==> Installing votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh >> ==> No binary for votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh found: >> installing from source >> ==> Fetching >> https://mirror.spack.io/_source-cache/archive/79/7991137098ff4511f4ca2c6f1b6c45f53d92d9f84e5c0d0e32fbc31768f73a83.tar.gz >> ==> No patches needed for votca >> ==> votca: Executing phase: 'cmake' >> ==> votca: Executing phase: 'build' >> ==> Error: ProcessError: Command exited with status 2: >> 'make' '-j16' >> 4 errors found in build log: >> >> ============== ERROR MESSAGE STARTS HERE ======================= >> >> 1414 cd >> /tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2/xtp/src/libxtp >> >> && /scratch/gpfs/satyend/ >> >> VOTCA_spack/spack/lib/spack/env/gcc/g++ -DBOOST_ATOMIC_DYN_LINK >> -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB >> -DBOOST_FILE >> >> SYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB >> -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB >> -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM >> >> _NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -Dvotca_xtp_EXPORTS >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspq >> >> kfaobeh7oh/spack-build-haft7z2/xtp/src/libxtp >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/xtp/s >> >> >> >> rc/libxtp >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/xtp/include >> >> -I/scratch/gpfs/satyend/VOTCA >> >> _spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/hdf5-1.12.1-earimxvbjgbi2afm4ibrzfxxnid3ftcp/include >> >> -I/tmp/satyend/spack-stage/spac >> >> k-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2/xtp/include >> >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4a >> >> rx2itjszbspqkfaobeh7oh/spack-build-haft7z2/xtp/include/votca/xtp >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh >> >> >> >> 7oh/spack-src/csg/include >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/tools/include >> >> -I/tmp/saty >> >> end/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2/tools/include >> >> -I/tmp/satyend/spack-stage/spack-stage >> >> -votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2/tools/include/votca/tools >> >> -isystem /scratch/gpfs/satyend/VOTCA_spack/spack/opt/ >> >> spack/linux-rhel8-skylake_avx512/gcc-8.5.0/boost-1.78.0-kpxditm3jxzcfmjnrukp3sclgydpkbn7/include >> >> -isystem /scratch/gpfs/satyend/VOTCA_spack/spac >> >> k/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/eigen-3.4.0-6rde23r6gr2p3zvfz2xb4zdgdmkuzbi2/include/eigen3 >> >> -isystem /scratch/gpfs/satyend/VOTC >> >> A_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/fftw-3.3.10-exhupro2fbjcelooay6xpafglbashmmy/include >> >> -isystem /scratch/gpfs/satyend >> >> /VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/libxc-5.1.7-fpxeg3vxgdtecmc2c72shnssrewzonuu/include >> >> -isystem /scratch/gpfs/sa >> >> tyend/VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/libint-2.6.0-tlcj2fdmzqzisgjqc6dhdlb64aqwy6oh/include >> >> -isystem /scratch/g >> >> pfs/satyend/VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/libecpint-1.0.5-avvfllm7bictbjttssrqyydxdwlfdmw4/include/libecpint >> >> >> >> -isystem >> /scratch/gpfs/satyend/VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/libecpint-1.0.5-avvfllm7bictbjttssrqyydxdwlfdmw4 >> >> >> >> /include -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native -O2 >> -g -DNDEBUG -fPIC -fopenmp -std=c++17 -MD -MT xtp/src/libxtp/CMakeFile >> >> s/votca_xtp.dir/trustregion.cc.o -MF >> CMakeFiles/votca_xtp.dir/trustregion.cc.o.d -o >> CMakeFiles/votca_xtp.dir/trustregion.cc.o -c /tmp/satyend/sp >> >> ack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/xtp/src/libxtp/trustregion.cc >> >> >> >> 1415 [ 93%] Building CXX object >> xtp/src/libxtp/CMakeFiles/votca_xtp.dir/version.cc.o >> >> 1416 cd >> /tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2/xtp/src/libxtp >> >> && /scratch/gpfs/satyend/ >> >> VOTCA_spack/spack/lib/spack/env/gcc/g++ -DBOOST_ATOMIC_DYN_LINK >> -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB >> -DBOOST_FILE >> >> SYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB >> -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB >> -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM >> >> _NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -Dvotca_xtp_EXPORTS >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspq >> >> kfaobeh7oh/spack-build-haft7z2/xtp/src/libxtp >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/xtp/s >> >> >> >> rc/libxtp >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/xtp/include >> >> -I/scratch/gpfs/satyend/VOTCA >> >> _spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/hdf5-1.12.1-earimxvbjgbi2afm4ibrzfxxnid3ftcp/include >> >> -I/tmp/satyend/spack-stage/spac >> >> k-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2/xtp/include >> >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4a >> >> rx2itjszbspqkfaobeh7oh/spack-build-haft7z2/xtp/include/votca/xtp >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh >> >> >> >> 7oh/spack-src/csg/include >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/tools/include >> >> -I/tmp/saty >> >> end/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2/tools/include >> >> -I/tmp/satyend/spack-stage/spack-stage >> >> -votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2/tools/include/votca/tools >> >> -isystem /scratch/gpfs/satyend/VOTCA_spack/spack/opt/ >> >> spack/linux-rhel8-skylake_avx512/gcc-8.5.0/boost-1.78.0-kpxditm3jxzcfmjnrukp3sclgydpkbn7/include >> >> -isystem /scratch/gpfs/satyend/VOTCA_spack/spac >> >> k/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/eigen-3.4.0-6rde23r6gr2p3zvfz2xb4zdgdmkuzbi2/include/eigen3 >> >> -isystem /scratch/gpfs/satyend/VOTC >> >> A_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/fftw-3.3.10-exhupro2fbjcelooay6xpafglbashmmy/include >> >> -isystem /scratch/gpfs/satyend >> >> /VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/libxc-5.1.7-fpxeg3vxgdtecmc2c72shnssrewzonuu/include >> >> -isystem /scratch/gpfs/sa >> >> tyend/VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/libint-2.6.0-tlcj2fdmzqzisgjqc6dhdlb64aqwy6oh/include >> >> -isystem /scratch/g >> >> pfs/satyend/VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/libecpint-1.0.5-avvfllm7bictbjttssrqyydxdwlfdmw4/include/libecpint >> >> >> >> -isystem >> /scratch/gpfs/satyend/VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/libecpint-1.0.5-avvfllm7bictbjttssrqyydxdwlfdmw4 >> >> >> >> /include -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native -O2 >> -g -DNDEBUG -fPIC -fopenmp -std=c++17 -MD -MT xtp/src/libxtp/CMakeFile >> >> s/votca_xtp.dir/version.cc.o -MF CMakeFiles/votca_xtp.dir/version.cc.o.d >> -o CMakeFiles/votca_xtp.dir/version.cc.o -c /tmp/satyend/spack-stage/sp >> >> ack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/xtp/src/libxtp/version.cc >> >> >> >> 1417 [ 94%] Building CXX object >> xtp/src/libxtp/CMakeFiles/votca_xtp.dir/xtpapplication.cc.o >> >> 1418 cd >> /tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2/xtp/src/libxtp >> >> && /scratch/gpfs/satyend/ >> >> VOTCA_spack/spack/lib/spack/env/gcc/g++ -DBOOST_ATOMIC_DYN_LINK >> -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB >> -DBOOST_FILE >> >> SYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB >> -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB >> -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM >> >> _NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -Dvotca_xtp_EXPORTS >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspq >> >> kfaobeh7oh/spack-build-haft7z2/xtp/src/libxtp >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/xtp/s >> >> >> >> rc/libxtp >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/xtp/include >> >> -I/scratch/gpfs/satyend/VOTCA >> >> _spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/hdf5-1.12.1-earimxvbjgbi2afm4ibrzfxxnid3ftcp/include >> >> -I/tmp/satyend/spack-stage/spac >> >> k-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2/xtp/include >> >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4a >> >> rx2itjszbspqkfaobeh7oh/spack-build-haft7z2/xtp/include/votca/xtp >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh >> >> >> >> 7oh/spack-src/csg/include >> -I/tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/tools/include >> >> -I/tmp/saty >> >> end/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2/tools/include >> >> -I/tmp/satyend/spack-stage/spack-stage >> >> -votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2/tools/include/votca/tools >> >> -isystem /scratch/gpfs/satyend/VOTCA_spack/spack/opt/ >> >> spack/linux-rhel8-skylake_avx512/gcc-8.5.0/boost-1.78.0-kpxditm3jxzcfmjnrukp3sclgydpkbn7/include >> >> -isystem >> /scratch/gpfs/satyend/VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/eigen-3.4.0-6rde23r6gr2p3zvfz2xb4zdgdmkuzbi2/include/eigen3 >> >> -isystem >> /scratch/gpfs/satyend/VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/fftw-3.3.10-exhupro2fbjcelooay6xpafglbashmmy/include >> >> -isystem >> /scratch/gpfs/satyend/VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/libxc-5.1.7-fpxeg3vxgdtecmc2c72shnssrewzonuu/include >> >> -isystem >> /scratch/gpfs/satyend/VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/libint-2.6.0-tlcj2fdmzqzisgjqc6dhdlb64aqwy6oh/include >> >> -isystem >> /scratch/gpfs/satyend/VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/libecpint-1.0.5-avvfllm7bictbjttssrqyydxdwlfdmw4/include/libecpint-isystem >> >> /scratch/gpfs/satyend/VOTCA_spack/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/libecpint-1.0.5-avvfllm7bictbjttssrqyydxdwlfdmw4 >> /include -Wall -Wextra -Wpedantic -Wshadow -Wconversion -march=native -O2 >> -g -DNDEBUG -fPIC -fopenmp -std=c++17 -MD -MT >> xtp/src/libxtp/CMakeFiles/votca_xtp.dir/xtpapplication.cc.o -MF >> CMakeFiles/votca_xtp.dir/xtpapplication.cc.o.d -o >> CMakeFiles/votca_xtp.dir/xtpapplication.cc.o -c /tmp/s >> >> atyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/xtp/src/libxtp/xtpapplication.cc >> 1419 >> /tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/xtp/src/libxtp/tools/gpu_benchmark.cc: >> >> In function 'std::pair<double, double> votca::xtp::CalcStatistics(const >> std::vector<double>&)': >> >> 1420 >> /tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/xtp/src/libxtp/tools/gpu_benchmark.cc:45:22: >> >> error: ' >> reduce' is not a member of 'std' >> 1421 double mean = std::reduce(v.begin(), v.end()) / ((double)v.size()); >> 1422 ^~~~~~ >> 1423 >> /tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-src/xtp/src/libxtp/tools/gpu_benchmark.cc:45:22: >> >> note: suggested alternative: 'replace' >> 1424 double mean = std::reduce(v.begin(), v.end()) / ((double)v.size()); >> 1425 ^~~~~~ >> 1426 replace >> >> 1427 make[2]: *** >> [xtp/src/libxtp/CMakeFiles/votca_xtp.dir/build.make:1843: >> xtp/src/libxtp/CMakeFiles/votca_xtp.dir/tools/gpu_benchmark.cc.o] Error 1 >> 1428 make[2]: *** Waiting for unfinished jobs.... >> 1429 make[2]: Leaving directory >> '/tmp/satyend/spack-stage/spack-stage-votca-2022haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2' >> >> 1430 make[1]: *** [CMakeFiles/Makefile2:3179: >> xtp/src/libxtp/CMakeFiles/votca_xtp.dir/all] Error 2 >> 1431 make[1]: Leaving directory >> '/tmp/satyend/spack-stage/spack-stage-votca-2022haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-haft7z2' >> >> 1432 make: *** [Makefile:139: all] Error 2 >> See build log for details: >> >> /tmp/satyend/spack-stage/spack-stage-votca-2022-haft7z2c4arx2itjszbspqkfaobeh7oh/spack-build-out.txt >> >> ============================================== >> >> What is the nature of this error message? How do I resolve this? >> > > I think your compiler is just too old, so if you a new one try that. > > I will try to add an xtp variant to spack, so you can compiler less. > > Christoph > >> >> On Thursday, February 17, 2022 at 8:36:24 PM UTC-5 Christoph Junghans >> wrote: >> >>> On Thu, Feb 17, 2022 at 5:49 PM Satyen Dhamankar <[email protected]> >>> wrote: >>> > >>> > Hello, >>> > >>> > I am getting VOTCA on a new system, and I am using Spack to obtain all >>> the dependencies. This is done with: >>> > git clone https://github.com/spack/spack.git spack >>> > source spack/share/spack/setup-env.sh >>> > spack install votca-csg@stable >>> After the latest release please use "spack install votca" instead. >>> >>> The other votca-* package are marked deprecated in spack now, I really >>> need to update the documentation, see: >>> https://github.com/votca/votca/pull/972 >>> >>> > >>> > However, I do not see the tutorials being pulled from the repo when I >>> do the above. >>> > >>> > I have the following questions: >>> > 1. How do I pull the csg-tutorials directory and run the tutorials to >>> check if VOTCA is running accurately? >>> When you build the "votca" package csg-tutorials will be installed as >>> well. >>> You can test your install by using "spack install --test root votca" >>> during the build. >>> >>> > 2. Once I have the tutorials, I assume I have to make sure I can run >>> the commands from terminal. What is the directory that must be added to >>> path? >>> > I see that >>> > >>> > >>> VOTCA/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/votca-csg-stable-bwf5m4a72i7zn7rnbttdnbsqgs7aq62j/bin >>> >>> >>> > >>> > is the location where all of the votca executables are: csg_boltzmann, >>> csg_inverse, csg_fmatch, etc. >>> > >>> > Is this the only location I add to path? Or are there other things I >>> must add to path to run VOTCA correctly? >>> Yeah you could add that to your path or just use "spack load votca" >>> >>> Christoph >>> > >>> > -- >>> > Join us on Slack: https://join.slack.com/t/votca/signup >>> > --- >>> > You received this message because you are subscribed to the Google >>> Groups "votca" group. >>> >> > To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> > To view this discussion on the web visit >>> https://groups.google.com/d/msgid/votca/137b542f-d0a3-419b-b328-55a46e668e82n%40googlegroups.com. >>> >>> >>> >>> >>> >>> -- >>> Christoph Junghans >>> Web: http://www.compphys.de >>> >> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/5d9a31f1-ad65-4fbe-a80c-0d0432867a42n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/votca/5d9a31f1-ad65-4fbe-a80c-0d0432867a42n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- > Christoph Junghans > Web: http://www.compphys.de > -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/9fda9345-8f33-45d7-9213-44bbde1a87ebn%40googlegroups.com.
