How to run VOTCA after installing via Spack

[Satyen Dhamankar]

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

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? 

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? 

[Christoph Junghans]

On Thu, Feb 17, 2022 at 5:49 PM Satyen Dhamankar <saty...@gmail.com> 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 votca+un...@googlegroups.com.
> 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

[Satyen Dhamankar]

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? 

[Christoph Junghans]

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 

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/5d9a31f1-ad65-4fbe-a80c-0d0432867a42n%40googlegroups.com.

[Satyen Dhamankar]

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. 

[Christoph Junghans]

On Mon, Feb 21, 2022 at 10:00 AM Satyen Dhamankar <saty...@gmail.com> wrote:
>
> 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.

The spack update (https://github.com/spack/spack/pull/29056) just to
merged, so you should now also be able to do:
$ spack install votca~xtp
to build votca with xtp, i.e. only the coarse-graining parts.

Cheers,

Christoph

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/9fda9345-8f33-45d7-9213-44bbde1a87ebn%40googlegroups.com.