SIESTA

Description: SIESTA performs electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

URL: https://departments.icmab.es/leem/siesta/

Team: Garotes de Premià

Compilation

Spack Package Modification

Details of any changes to the Spack recipe used.

Git commit hash of checkout for pacakage: b4cd913

Pull request for Spack recipe changes: spack/spack#24937

Building SIESTA

GNU Fortran Compiler (GNU)

spack install siesta@4.0.1%gcc@10.3.0+metis

$ spack spec -Il siesta@4.0.1%gcc@10.3.0+metis
Input spec
 -   siesta@4.0.1%gcc@10.3.0+metis

Concretized
--------------------------------
[+]  e374e4q  siesta@4.0.1%gcc@10.3.0+metis patches=b8f722add750b1524767062c7a86de63a1da7990c27fda5321e43e34179e50fc arch=linux-amzn2-graviton2
[+]  a3tjh3r      ^metis@5.1.0%gcc@10.3.0~gdb~int64~real64+shared build_type=Release patches=4991da938c1d3a1d3dea78e49bbebecba00273f98df2a656e38b83d55b281da1,b1225da886605ea558db7ac08dd8054742ea5afe5ed61ad4d0fe7a495b1270d2 arch=linux-amzn2-graviton2
[+]  m7325ee          ^cmake@3.20.5%gcc@10.3.0~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-amzn2-graviton2
[+]  iwzirqc              ^ncurses@6.2%gcc@10.3.0~symlinks+termlib abi=none arch=linux-amzn2-graviton2
[+]  s4pw7zm                  ^pkgconf@1.7.4%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  5i3lgfb              ^openssl@1.1.1k%gcc@10.3.0~docs+systemcerts arch=linux-amzn2-graviton2
[+]  4m7exgb                  ^perl@5.32.1%gcc@10.3.0+cpanm+shared+threads arch=linux-amzn2-graviton2
[+]  y42m6yr                      ^berkeley-db@18.1.40%gcc@10.3.0+cxx~docs+stl patches=b231fcc4d5cff05e5c3a4814f6a5af0e9a966428dc2176540d2c05aff41de522 arch=linux-amzn2-graviton2
[+]  rqrpmap                      ^bzip2@1.0.8%gcc@10.3.0~debug~pic+shared arch=linux-amzn2-graviton2
[+]  2w7bert                          ^diffutils@3.7%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  y5ei3cm                              ^libiconv@1.16%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  wjwqncx                      ^gdbm@1.19%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  3zy7kxk                          ^readline@8.1%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  qepjcvj                      ^zlib@1.2.11%gcc@10.3.0+optimize+pic+shared arch=linux-amzn2-graviton2
[+]  tfzbzgi      ^netcdf-c@4.8.0%gcc@10.3.0~dap~fsync~hdf4~jna+mpi~parallel-netcdf+pic+shared arch=linux-amzn2-graviton2
[+]  cg7z7ep          ^hdf5@1.10.7%gcc@10.3.0~cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo arch=linux-amzn2-graviton2
[+]  zvamksn              ^openmpi@4.1.0%gcc@10.3.0~atomics~cuda~cxx~cxx_exceptions+gpfs~internal-hwloc~java~legacylaunchers~lustre~memchecker+pmi~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=ofi patches=60ce20bc14d98c572ef7883b9fcd254c3f232c2f3a13377480f96466169ac4c8 schedulers=slurm arch=linux-amzn2-graviton2
[+]  cukmqbg                  ^hwloc@2.5.0%gcc@10.3.0~cairo~cuda~gl~libudev+libxml2~netloc~nvml+pci+shared arch=linux-amzn2-graviton2
[+]  asgtk6a                      ^libpciaccess@0.16%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  z2uysov                          ^libtool@2.4.6%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  ebhjpix                              ^m4@1.4.18%gcc@10.3.0+sigsegv patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 arch=linux-amzn2-graviton2
[+]  ltbv6bk                                  ^libsigsegv@2.13%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  4xr3hhh                          ^util-macros@1.19.3%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  iyhm3wi                      ^libxml2@2.9.10%gcc@10.3.0~python arch=linux-amzn2-graviton2
[+]  ye3kcvv                          ^xz@5.2.5%gcc@10.3.0~pic libs=shared,static arch=linux-amzn2-graviton2
[+]  tadxrfp                  ^libevent@2.1.12%gcc@10.3.0+openssl arch=linux-amzn2-graviton2
[+]  72f5gvk                  ^libfabric@1.11.1-aws%gcc@10.3.0~debug~kdreg fabrics=sockets,tcp,udp arch=linux-amzn2-graviton2
[+]  mhav5gn                  ^numactl@2.0.14%gcc@10.3.0 patches=4e1d78cbbb85de625bad28705e748856033eaafab92a66dffd383a3d7e00cc94,62fc8a8bf7665a60e8f4c93ebbd535647cebf74198f7afafec4c085a8825c006 arch=linux-amzn2-graviton2
[+]  jkuhz64                      ^autoconf@2.69%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  xb2w5nc                      ^automake@1.16.3%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  wturp6c                  ^openssh@8.5p1%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  ivotdt7                      ^libedit@3.1-20210216%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  wqpuvmh                  ^slurm@20-02-4-1%gcc@10.3.0~gtk~hdf5~hwloc~mariadb~pmix+readline~restd sysconfdir=PREFIX/etc arch=linux-amzn2-graviton2
[+]  6ku6khi      ^netcdf-fortran@4.5.3%gcc@10.3.0~doc+pic+shared arch=linux-amzn2-graviton2
[+]  2jffbna      ^netlib-scalapack@2.1.0%gcc@10.3.0~ipo~pic+shared build_type=Release patches=1c9ce5fee1451a08c2de3cc87f446aeda0b818ebbce4ad0d980ddf2f2a0b2dc4,f2baedde688ffe4c20943c334f580eb298e04d6f35c86b90a1f4e8cb7ae344a2 arch=linux-amzn2-graviton2
[+]  rv7gj6u          ^openblas@0.3.15%gcc@10.3.0~bignuma~consistent_fpcsr~ilp64+locking+pic+shared threads=none arch=linux-amzn2-graviton2

ARM and Nvidia HPC Compilers

Unfortunetly we could not compile siesta with neither the ARM compiler nor the Nvidia one.

On both compilers the compilation ends with the same error, after solving all the other errors we encountered. The error is due to multiple definitions of mpi_comm_world, and we were not able to find a solution. The error:

==> siesta: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
    'make'

2 errors found in build log:
     355    NVFORTRAN-S-0155-mpi_comm_world is use-associated from modules mpi_siesta and mpi__include, and cannot be accessed (/tmp/jvinyals/spack-stage/spack-stage-siesta-4.0.1-emukb7kkp46sefjkkzjt5nafsfai54l7/spack-src/Src/fdf/fdf
            .F90: 2829)
     356    NVFORTRAN-S-0155-mpi_comm_world is use-associated from modules mpi_siesta and mpi__include, and cannot be accessed (/tmp/jvinyals/spack-stage/spack-stage-siesta-4.0.1-emukb7kkp46sefjkkzjt5nafsfai54l7/spack-src/Src/fdf/fdf
            .F90: 2837)
     357      0 inform,   0 warnings,   2 severes, 0 fatal for fdf_sendinput
     358    NVFORTRAN-S-0155-mpi_comm_world is use-associated from modules mpi_siesta and mpi__include, and cannot be accessed (/tmp/jvinyals/spack-stage/spack-stage-siesta-4.0.1-emukb7kkp46sefjkkzjt5nafsfai54l7/spack-src/Src/fdf/fdf
            .F90: 2868)
     359    NVFORTRAN-S-0155-mpi_comm_world is use-associated from modules mpi_siesta and mpi__include, and cannot be accessed (/tmp/jvinyals/spack-stage/spack-stage-siesta-4.0.1-emukb7kkp46sefjkkzjt5nafsfai54l7/spack-src/Src/fdf/fdf
            .F90: 2881)
     360      0 inform,   0 warnings,   2 severes, 0 fatal for fdf_recvinput
  >> 361    make[1]: *** [fdf.o] Error 2
     362    make[1]: Leaving directory `/tmp/jvinyals/spack-stage/spack-stage-siesta-4.0.1-emukb7kkp46sefjkkzjt5nafsfai54l7/spack-src/Obj/fdf'
  >> 363    make: *** [libfdf.a] Error 2

ARM

Our first try was using the spack install command as below, only specifying the compiler. This did not work.

spack install siesta%arm

The first error we found in whilst compiling with the ARM compiler was a module overload by the siesta code. The code overloaded the iso_fortran_env. To solve these we added in the configure phase two commands to rename the module to siesta_fortran_env.

def configure(self, spec, prefix):
        
        ...        

        sh("-c", "find -type  f -exec sed -i 's/iso_fortran_env/siesta_fortran_env/g' {} \\;")
        sh("-c", "find -iname iso_fortran_env.F90 -exec rename iso siesta {} \\;
        
        ...

This solved the problem leading us to the final problem with this compiler (mentioned avove). Leaving the final spec of our attempt to install it as shown below.

$ spack spec -Il siesta%arm

Input spec
--------------------------------
 -   siesta%arm

Concretized
--------------------------------
==> Warning: arm@21.0.0.879 cannot build optimized binaries for "graviton2". Using best target possible: "aarch64"
 -   564l6xo  siesta@4.0.1%arm@21.0.0.879~metis patches=b8f722add750b1524767062c7a86de63a1da7990c27fda5321e43e34179e50fc arch=linux-amzn2-aarch64
[+]  32qnomy      ^netcdf-c@4.8.0%arm@21.0.0.879~dap~fsync~hdf4~jna+mpi~parallel-netcdf+pic+shared arch=linux-amzn2-aarch64
[+]  e4dajf6          ^hdf5@1.10.7%arm@21.0.0.879~cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo arch=linux-amzn2-aarch64
[+]  fqvybaf              ^cmake@3.20.5%arm@21.0.0.879~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-amzn2-aarch64
[+]  uhtqtlb                  ^ncurses@6.2%arm@21.0.0.879~symlinks+termlib abi=none arch=linux-amzn2-aarch64
[+]  zpuzm23                      ^pkgconf@1.7.4%arm@21.0.0.879 arch=linux-amzn2-aarch64
[+]  vc3waha                  ^openssl@1.1.1k%arm@21.0.0.879~docs+systemcerts arch=linux-amzn2-aarch64
[+]  vv6txro                      ^perl@5.32.1%arm@21.0.0.879+cpanm+shared+threads arch=linux-amzn2-aarch64
[+]  33wiajj                          ^berkeley-db@18.1.40%arm@21.0.0.879+cxx~docs+stl patches=b231fcc4d5cff05e5c3a4814f6a5af0e9a966428dc2176540d2c05aff41de522 arch=linux-amzn2-aarch64
[+]  z4ybgri                          ^bzip2@1.0.8%arm@21.0.0.879~debug~pic+shared arch=linux-amzn2-aarch64
[+]  adtc6yc                              ^diffutils@3.7%arm@21.0.0.879 arch=linux-amzn2-aarch64
[+]  7vnthzn                                  ^libiconv@1.16%arm@21.0.0.879 arch=linux-amzn2-aarch64
[+]  645q4qj                          ^gdbm@1.19%arm@21.0.0.879 arch=linux-amzn2-aarch64
[+]  3haw5gt                              ^readline@8.1%arm@21.0.0.879 arch=linux-amzn2-aarch64
[+]  puuxvg2                          ^zlib@1.2.11%arm@21.0.0.879+optimize+pic+shared arch=linux-amzn2-aarch64
[+]  lmaoy5t              ^openmpi@4.1.0%arm@21.0.0.879~atomics~cuda~cxx~cxx_exceptions+gpfs~internal-hwloc~java~legacylaunchers~lustre~memchecker+pmi~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=ofi patches=60ce20bc14d98c572ef7883b9fcd254c3f232c2f3a13377480f96466169ac4c8 schedulers=slurm arch=linux-amzn2-aarch64
[+]  xl6anaa                  ^hwloc@2.5.0%arm@21.0.0.879~cairo~cuda~gl~libudev+libxml2~netloc~nvml+pci+shared arch=linux-amzn2-aarch64
[+]  jueqz7p                      ^libpciaccess@0.16%arm@21.0.0.879 arch=linux-amzn2-aarch64
[+]  e4ssqx6                          ^libtool@2.4.6%arm@21.0.0.879 arch=linux-amzn2-aarch64
[+]  i2jmeo4                              ^m4@1.4.18%arm@21.0.0.879+sigsegv patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 arch=linux-amzn2-aarch64
[+]  6jhzlul                                  ^libsigsegv@2.13%arm@21.0.0.879 arch=linux-amzn2-aarch64
[+]  uwcxkin                          ^util-macros@1.19.3%arm@21.0.0.879 arch=linux-amzn2-aarch64
[+]  dypqz2i                      ^libxml2@2.9.10%arm@21.0.0.879~python arch=linux-amzn2-aarch64
[+]  zqsab4f                          ^xz@5.2.5%arm@21.0.0.879~pic libs=shared,static arch=linux-amzn2-aarch64
[+]  gonqskn                  ^libevent@2.1.12%arm@21.0.0.879+openssl arch=linux-amzn2-aarch64
[+]  qdn27nh                  ^libfabric@1.11.1-aws%arm@21.0.0.879~debug~kdreg fabrics=sockets,tcp,udp arch=linux-amzn2-aarch64
[+]  mv2g7r5                  ^numactl@2.0.14%arm@21.0.0.879 patches=4e1d78cbbb85de625bad28705e748856033eaafab92a66dffd383a3d7e00cc94,62fc8a8bf7665a60e8f4c93ebbd535647cebf74198f7afafec4c085a8825c006 arch=linux-amzn2-aarch64
[+]  dcs645r                      ^autoconf@2.69%arm@21.0.0.879 arch=linux-amzn2-aarch64
[+]  edezkz3                      ^automake@1.16.3%arm@21.0.0.879 arch=linux-amzn2-aarch64
[+]  6vvthuo                  ^openssh@8.5p1%arm@21.0.0.879 arch=linux-amzn2-aarch64
[+]  xe4evc4                      ^libedit@3.1-20210216%arm@21.0.0.879 arch=linux-amzn2-aarch64
[+]  x5xehti                  ^slurm@20-02-4-1%arm@21.0.0.879~gtk~hdf5~hwloc~mariadb~pmix+readline~restd sysconfdir=PREFIX/etc arch=linux-amzn2-aarch64
[+]  im5sbgn      ^netcdf-fortran@4.5.3%arm@21.0.0.879~doc+pic+shared arch=linux-amzn2-aarch64
[+]  xc2r6zp      ^netlib-scalapack@2.1.0%arm@21.0.0.879~ipo~pic+shared build_type=Release patches=1c9ce5fee1451a08c2de3cc87f446aeda0b818ebbce4ad0d980ddf2f2a0b2dc4,f2baedde688ffe4c20943c334f580eb298e04d6f35c86b90a1f4e8cb7ae344a2 arch=linux-amzn2-aarch64
[+]  cwuo4ek          ^openblas@0.3.15%arm@21.0.0.879~bignuma~consistent_fpcsr~ilp64+locking+pic+shared threads=none arch=linux-amzn2-aarch64

Nvidia HPC (NVHPC)

Our first aproach was again to simpli specify the Nvidia HPC Compiler. The problem with this module was a conflict with both cmake and openblas which weren compatibles with the compiler.

spack install siesta%nvhpc

Then we tried to compile these modules with the GNU Compiler, trying to get a binary, using the spack command below. This solved the conflicts, and lead us to the final error. Because we were not able to solve the mpi_comm_world problem, we did not try to patch the packages of the dependencies to compile with this compiler.

spack install siesta%nvhpc ^cmake%gcc ^openblas%gcc

The final spec of our attempt to compile it was as below.

$ spack spec -Il siesta%nvhpc ^cmake%gcc ^openblas%gcc

Input spec
--------------------------------
 -   siesta%nvhpc
 -       ^cmake%gcc
 -       ^openblas%gcc

Concretized
--------------------------------
 -   emukb7k  siesta@4.0.1%nvhpc@21.2~metis patches=b8f722add750b1524767062c7a86de63a1da7990c27fda5321e43e34179e50fc arch=linux-amzn2-graviton2
[+]  baltkx5      ^netcdf-c@4.8.0%nvhpc@21.2~dap~fsync~hdf4~jna+mpi~parallel-netcdf+pic+shared arch=linux-amzn2-graviton2
[+]  wwncepq          ^hdf5@1.10.7%nvhpc@21.2~cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo arch=linux-amzn2-graviton2
[+]  it4etcv              ^cmake@3.20.5%gcc@10.3.0~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-amzn2-graviton2
[+]  iwzirqc                  ^ncurses@6.2%gcc@10.3.0~symlinks+termlib abi=none arch=linux-amzn2-graviton2
[+]  s4pw7zm                      ^pkgconf@1.7.4%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  kssecxk                  ^openssl@1.1.1k%gcc@10.3.0~docs+systemcerts arch=linux-amzn2-graviton2
[+]  zyh3ju5                      ^perl@5.32.1%gcc@10.3.0+cpanm+shared+threads arch=linux-amzn2-graviton2
[+]  y42m6yr                          ^berkeley-db@18.1.40%gcc@10.3.0+cxx~docs+stl patches=b231fcc4d5cff05e5c3a4814f6a5af0e9a966428dc2176540d2c05aff41de522 arch=linux-amzn2-graviton2
[+]  rqrpmap                          ^bzip2@1.0.8%gcc@10.3.0~debug~pic+shared arch=linux-amzn2-graviton2
[+]  2w7bert                              ^diffutils@3.7%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  y5ei3cm                                  ^libiconv@1.16%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  wjwqncx                          ^gdbm@1.19%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  3zy7kxk                              ^readline@8.1%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  4js6ect                          ^zlib@1.2.11%nvhpc@21.2+optimize+pic+shared arch=linux-amzn2-graviton2
[+]  dc5i2vh              ^openmpi@4.1.0%nvhpc@21.2~atomics~cuda~cxx~cxx_exceptions+gpfs~internal-hwloc~java~legacylaunchers~lustre~memchecker+pmi~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=ofi patches=60ce20bc14d98c572ef7883b9fcd254c3f232c2f3a13377480f96466169ac4c8,fba0d3a784a9723338722b48024a22bb32f6a951db841a4e9f08930a93f41d7a schedulers=slurm arch=linux-amzn2-graviton2
[+]  euby7td                  ^hwloc@2.5.0%nvhpc@21.2~cairo~cuda~gl~libudev+libxml2~netloc~nvml+pci+shared arch=linux-amzn2-graviton2
[+]  e4m4ued                      ^libpciaccess@0.16%nvhpc@21.2 patches=6e08dc445ece06e9e8b1344397f2d3f169005703ddc0f2ae24f366cde78c7377 arch=linux-amzn2-graviton2
[+]  kk4ax3i                          ^libtool@2.4.6%nvhpc@21.2 arch=linux-amzn2-graviton2
[+]  6c4kz5g                              ^m4@1.4.18%nvhpc@21.2+sigsegv patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,5746cf51f45b405661c3edae7a78c33d41e54d83f635d16e2bf1f956dbfbf635,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 arch=linux-amzn2-graviton2
[+]  pa6wm5j                                  ^libsigsegv@2.13%nvhpc@21.2 arch=linux-amzn2-graviton2
[+]  4imdwuy                          ^util-macros@1.19.3%nvhpc@21.2 arch=linux-amzn2-graviton2
[+]  jzxyspx                      ^libxml2@2.9.10%nvhpc@21.2~python patches=05ff238cf435825ef835c7ae39376b52dc83d8caf19e962f0766c841386a305a,10a88ad47f9797cf7cf2d7d07241f665a3b6d1f31fa026728c8c2ae93e1664e9 arch=linux-amzn2-graviton2
[+]  br733tn                          ^xz@5.2.5%nvhpc@21.2~pic libs=shared,static arch=linux-amzn2-graviton2
[+]  qs5m2pb                  ^libevent@2.1.12%nvhpc@21.2+openssl arch=linux-amzn2-graviton2
[+]  xl6zavq                  ^libfabric@1.11.1-aws%nvhpc@21.2~debug~kdreg fabrics=sockets,tcp,udp arch=linux-amzn2-graviton2
[+]  5yq4tpw                  ^numactl@2.0.14%nvhpc@21.2 patches=4e1d78cbbb85de625bad28705e748856033eaafab92a66dffd383a3d7e00cc94,62fc8a8bf7665a60e8f4c93ebbd535647cebf74198f7afafec4c085a8825c006 arch=linux-amzn2-graviton2
[+]  dghtild                      ^autoconf@2.69%nvhpc@21.2 arch=linux-amzn2-graviton2
[+]  umo35bq                      ^automake@1.16.3%nvhpc@21.2 arch=linux-amzn2-graviton2
[+]  tydb3k5                  ^openssh@8.5p1%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  ivotdt7                      ^libedit@3.1-20210216%gcc@10.3.0 arch=linux-amzn2-graviton2
[+]  zehhooy                  ^slurm@20-02-4-1%nvhpc@21.2~gtk~hdf5~hwloc~mariadb~pmix+readline~restd sysconfdir=PREFIX/etc arch=linux-amzn2-graviton2
[+]  vekbvrj      ^netcdf-fortran@4.5.3%nvhpc@21.2~doc+pic+shared arch=linux-amzn2-graviton2
[+]  5vrjohv      ^netlib-scalapack@2.1.0%nvhpc@21.2~ipo~pic+shared build_type=Release patches=1c9ce5fee1451a08c2de3cc87f446aeda0b818ebbce4ad0d980ddf2f2a0b2dc4,f2baedde688ffe4c20943c334f580eb298e04d6f35c86b90a1f4e8cb7ae344a2 arch=linux-amzn2-graviton2
[+]  rv7gj6u          ^openblas@0.3.15%gcc@10.3.0~bignuma~consistent_fpcsr~ilp64+locking+pic+shared threads=none arch=linux-amzn2-graviton2

Test Case 1

ReFrame Benchmark 1

$ reframe -c job.onnode.py -r --performance-report

Validation

The only validation that we do is check that the execution finishes without error. We used this method because we did not know about the science behind, and were not able to find validation data.

ReFrame Output

On-node

==============================================================================
PERFORMANCE REPORT
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_2_OMP_1
- aws:c6gn
   - builtin
      * num_tasks: 2
      * Run Time: 1356.59 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_4_OMP_1
   - builtin
      * num_tasks: 4
      * Run Time: 753.26 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_8_OMP_1
   - builtin
      * num_tasks: 8
      * Run Time: 435.4 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_16_OMP_1
   - builtin
      * num_tasks: 16
      * Run Time: 280.76 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_32_OMP_1
   - builtin
      * num_tasks: 32
      * Run Time: 187.52 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_64_OMP_1
   - builtin
      * num_tasks: 64
      * Run Time: 151.42 None
------------------------------------------------------------------------------

Off-node

==============================================================================
PERFORMANCE REPORT
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_8_OMP_1
- aws:c6gn
   - builtin
      * num_tasks: 8
      * Run Time: 430.85 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_16_OMP_1
   - builtin
      * num_tasks: 16
      * Run Time: 278.13 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_32_OMP_1
   - builtin
      * num_tasks: 32
      * Run Time: 185.62 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_64_OMP_1
   - builtin
      * num_tasks: 64
      * Run Time: 152.54 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_2_MPI_128_OMP_1
   - builtin
      * num_tasks: 128
      * Run Time: 230.6 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_4_MPI_256_OMP_1
   - builtin
      * num_tasks: 256
      * Run Time: 306.58 None

430.85 278.13 185.62 152.54 230.60 306.58

On-node Compiler Comparison

Performance comparison of two compilers.

Cores	GNU
2	1356.59
4	753.26
8	435.40
16	280.76
32	187.52
64	151.52

Strong Scaling Study

On-node scaling study for the GNU Compiler.

Cores	GNU
2	1356.59
4	753.26
8	435.40
16	280.76
32	187.52
64	151.52

On-Node Architecture Comparison

On-node scaling study for two architectures.

The c6ng on-node reframe report is the same one seent above in the # On-node section.

The c5n on-node reframe report:

[==========] Finished on Fri Jul 16 20:29:06 2021 
==============================================================================
PERFORMANCE REPORT
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_2_OMP_1
- aws:c5n
   - builtin
      * num_tasks: 2
      * Run Time: 1385.13 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_4_OMP_1
   - builtin
      * num_tasks: 4
      * Run Time: 782.3 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_8_OMP_1
   - builtin
      * num_tasks: 8
      * Run Time: 457.13 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_16_OMP_1
   - builtin
      * num_tasks: 16
      * Run Time: 298.04 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_32_OMP_1
   - builtin
      * num_tasks: 32
      * Run Time: 205.45 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_64_OMP_1
   - builtin
      * num_tasks: 64
      * Run Time: 160.11 None
------------------------------------------------------------------------------

The scalability comparison betwen architectures on-node.

Cores	C6gn (Aarch64)	C5n (X86)
2	430.85	1385.13
4	278.13	782.30
8	185.62	457.13
16	152.54	298.04
32	230.60	205.45
64	306.58	160.11

The c6ng off-node reframe report:

==============================================================================
PERFORMANCE REPORT
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_8_OMP_1
- aws:c6gn
   - builtin
      * num_tasks: 8
      * Run Time: 434.38 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_16_OMP_1
   - builtin
      * num_tasks: 16
      * Run Time: 279.96 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_32_OMP_1
   - builtin
      * num_tasks: 32
      * Run Time: 187.25 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_64_OMP_1
   - builtin
      * num_tasks: 64
      * Run Time: 150.2 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_2_MPI_128_OMP_1
   - builtin
      * num_tasks: 128
      * Run Time: 237.7 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_4_MPI_256_OMP_1
   - builtin
      * num_tasks: 256
      * Run Time: 327.59 None
------------------------------------------------------------------------------

The c5n off-node reframe report:

==============================================================================
PERFORMANCE REPORT
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_8_OMP_1
- aws:c5n
   - builtin
      * num_tasks: 8
      * Run Time: 459.34 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_16_OMP_1
   - builtin
      * num_tasks: 16
      * Run Time: 301.42 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_32_OMP_1
   - builtin
      * num_tasks: 32
      * Run Time: 208.06 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_1_MPI_64_OMP_1
   - builtin
      * num_tasks: 64
      * Run Time: 161.46 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_2_MPI_128_OMP_1
   - builtin
      * num_tasks: 128
      * Run Time: 343.96 None
------------------------------------------------------------------------------
SIESTA_Scalability h2o_64 input_siesta_4_0_1__gcc_10_3_0__metis_N_4_MPI_256_OMP_1
   - builtin
      * num_tasks: 256
      * Run Time: 417.51 None
------------------------------------------------------------------------------

The scalability comparison betwen architectures off-node.

Cores	Cores	C6gn (Aarch64)	C5n (X86)
1	8	434.38	459,34
1	16	239.68	301.42
1	32	187.25	208.06
1	64	150.20	161.46
2	128	237.70	343.96
4	256	327.59	417.51

Report

Compilation Summary

Siesta was an easy application to compile using the GNU Compiler, on the other hand using the ARM Compiler and the Nvidia HPC Compiler was not possible due to the code that implements siesta. It has some incompatible/non-standard module implementation that made it impossible for us to compile the aplication using said compailers.

Performance Summary

Siesta is an aplication that scales fairly well on-node, and when scaling off-node it starts to lose performance. Whereas we think that its scalaility is hardly related to the input set, we think there is space for improvement.

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README.md

README.md

SIESTA

Compilation

Spack Package Modification

Building SIESTA

GNU Fortran Compiler (GNU)

ARM and Nvidia HPC Compilers

ARM

Nvidia HPC (NVHPC)

Test Case 1

Validation

ReFrame Output

On-node

Off-node

On-node Compiler Comparison

Strong Scaling Study

On-Node Architecture Comparison

Report

Compilation Summary

Performance Summary

Files

README.md

Latest commit

History

README.md

File metadata and controls

SIESTA

Compilation

Spack Package Modification

Building SIESTA

GNU Fortran Compiler (GNU)

ARM and Nvidia HPC Compilers

ARM

Nvidia HPC (NVHPC)

Test Case 1

Validation

ReFrame Output

On-node

Off-node

On-node Compiler Comparison

Strong Scaling Study

On-Node Architecture Comparison

Report

Compilation Summary

Performance Summary