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/CAHG27e5QtSaQ4%2BqT1KjEr5CaZq3gpF8HUfrUFOhAD1VT%2ByR7GQ%40mail.gmail.com.
