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Assigned to lik...@wp.pl by me
daniele.barbera86
Dec 1, 2021, 11:08:59 AM12/1/21
to MoFEM Q&A
Dear all,
I was following the procedure for installing developer version of MoFEM on Buckethead however, I got stuck during the installation of the dependencies. In particular I stuck when installing sleep-3.11.2
==> Error: KeyError: 'No spec with name arpack-ng in sl...@3.11.2%g...@9.3.0+arpack~blopex (very long error)
/home/staff/db296a/spack/var/spack/repos/builtin/packages/slepc/package.py:98, in install:
95
96 if '+arpack' in spec:
97 options.extend([
>> 98 '--with-arpack-dir=%s' % spec['arpack-ng'].prefix.lib,
99 ])
100 if spec.satisfies('@:3.12.99'):
101 arpackopt = '--with-arpack-flags'
The log txt file just contain an e line that state the execution phase where the issue occurred, during installation. I tried also the user installation, in case something was not updated in the development, but I get the same error. Do you have any suggestion?
Cheers
daniele.barbera86
Dec 1, 2021, 11:23:52 AM12/1/21
to MoFEM Q&A
The full error
==> Error: KeyError: 'No spec with name arpack-ng in sl...@3.11.2%g...@9.3.0+arpack~blopex arch=linux-centos7-sandybridge ^berke...@18.1.40%g...@9.3.0 arch=linux-centos7-sandybridge ^bz...@1.0.8%g...@9.3.0+shared arch=linux-centos7-sandybridge ^cm...@3.18.4%g...@9.3.0~doc+ncurses+openssl+ownlibs~qt patches=bf695e3febb222da2ed94b3beea600650e4318975da90e4a71d6f31a6d5d8c3d arch=linux-centos7-sandybridge ^diffutils@3.7%g...@9.3.0 arch=linux-centos7-sandybridge ^ex...@2.2.10%g...@9.3.0+libbsd arch=linux-centos7-sandybridge ^gd...@1.18.1%g...@9.3.0 arch=linux-centos7-sandybridge ^get...@0.21%g...@9.3.0+bzip2+curses+git~libunistring+libxml2+tar+xz arch=linux-centos7-sandybridge ^hd...@1.10.7%g...@9.3.0~cxx~debug~fortran~hl~java+mpi+pic+shared~szip~threadsafe api=none arch=linux-centos7-sandybridge ^hy...@2.18.2%g...@9.3.0~complex~debug~int64~internal-superlu~mixedint+mpi~openmp+shared~superlu-dist patches=6e3336b1d62155f6350dfe42b0f9ea25d4fa0af60c7e540959139deb93a26059 arch=linux-centos7-sandybridge ^lib...@0.10.0%g...@9.3.0 arch=linux-centos7-sandybridge ^libffi@3.3%g...@9.3.0 patches=26f26c6f29a7ce9bf370ad3ab2610f99365b4bdd7b82e7c31df41a3370d685c0 arch=linux-centos7-sandybridge ^libi...@1.16%g...@9.3.0 arch=linux-centos7-sandybridge ^lib...@1.0.3%g...@9.3.0 arch=linux-centos7-sandybridge ^lib...@2.9.10%g...@9.3.0~python arch=linux-centos7-sandybridge ^me...@5.1.0%g...@9.3.0~gdb~int64~real64+shared build_type=Release patches=4991da938c1d3a1d3dea78e49bbebecba00273f98df2a656e38b83d55b281da1,b1225da886605ea558db7ac08dd8054742ea5afe5ed61ad4d0fe7a495b1270d2 arch=linux-centos7-sandybridge ^mu...@5.3.3%g...@9.3.0+complex+double+float~int64~metis+mpi~parmetis~ptscotch~scotch+shared arch=linux-centos7-sandybridge ^ncurses@6.2%g...@9.3.0~symlinks+termlib arch=linux-centos7-sandybridge ^netlib-s...@2.1.0%g...@9.3.0~ipo~pic+shared build_type=Release patches=1c9ce5fee1451a08c2de3cc87f446aeda0b818ebbce4ad0d980ddf2f2a0b2dc4,f2baedde688ffe4c20943c334f580eb298e04d6f35c86b90a1f4e8cb7ae344a2 arch=linux-centos7-sandybridge ^open...@0.3.12%g...@9.3.0~consistent_fpcsr~ilp64+pic+shared threads=none arch=linux-centos7-sandybridge ^ope...@3.1.6%g...@9.3.0~atomics~cuda~cxx~cxx_exceptions+gpfs~java~legacylaunchers~lustre~memchecker~pmi~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=none schedulers=none arch=linux-centos7-sandybridge ^ope...@1.1.1h%g...@9.3.0+systemcerts arch=linux-centos7-sandybridge ^parm...@4.0.3%g...@9.3.0~gdb~int64~ipo+shared build_type=RelWithDebInfo patches=4f892531eb0a807eb1b82e683a416d3e35154a455274cf9b162fb02054d11a5b,50ed2081bc939269689789942067c58b3e522c269269a430d5d34c00edbc5870,704b84f7c7444d4372cb59cca6e1209df4ef3b033bc4ee3cf50f369bce972a9d arch=linux-centos7-sandybridge ^pe...@5.32.0%g...@9.3.0+cpanm+shared+threads arch=linux-centos7-sandybridge ^pe...@3.11.4%g...@9.3.0~X~batch~cgns~complex~cuda~debug+double~exodusii~fftw~giflib+hdf5+hypre~int64~jpeg~knl~libpng~libyaml~memkind+metis~moab~mpfr+mpi+mumps~p4est~random123~saws+shared~suite-sparse+superlu-dist~trilinos~valgrind clanguage=C arch=linux-centos7-sandybridge ^pkg...@1.7.3%g...@9.3.0 arch=linux-centos7-sandybridge ^pyt...@3.8.6%g...@9.3.0+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib patches=0d98e93189bc278fbc37a50ed7f183bd8aaf249a8e1670a465f0db6bb4f8cf87 arch=linux-centos7-sandybridge ^readline@8.0%g...@9.3.0 arch=linux-centos7-sandybridge ^sql...@3.33.0%g...@9.3.0+column_metadata+fts~functions~rtree arch=linux-centos7-sandybridge ^superl...@6.1.1%g...@9.3.0~cuda~int64~ipo~openmp+shared build_type=RelWithDebInfo cuda_arch=none arch=linux-centos7-sandybridge ^t...@1.32%g...@9.3.0 arch=linux-centos7-sandybridge ^x...@5.2.5%g...@9.3.0~pic arch=linux-centos7-sandybridge ^zl...@1.2.11%g...@9.3.0+optimize+pic+shared arch=linux-centos7-sandybridge'
==> Error: KeyError: 'No spec with name arpack-ng in sl...@3.11.2%g...@9.3.0+arpack~blopex arch=linux-centos7-sandybridge ^berke...@18.1.40%g...@9.3.0 arch=linux-centos7-sandybridge ^bz...@1.0.8%g...@9.3.0+shared arch=linux-centos7-sandybridge ^cm...@3.18.4%g...@9.3.0~doc+ncurses+openssl+ownlibs~qt patches=bf695e3febb222da2ed94b3beea600650e4318975da90e4a71d6f31a6d5d8c3d arch=linux-centos7-sandybridge ^diffutils@3.7%g...@9.3.0 arch=linux-centos7-sandybridge ^ex...@2.2.10%g...@9.3.0+libbsd arch=linux-centos7-sandybridge ^gd...@1.18.1%g...@9.3.0 arch=linux-centos7-sandybridge ^get...@0.21%g...@9.3.0+bzip2+curses+git~libunistring+libxml2+tar+xz arch=linux-centos7-sandybridge ^hd...@1.10.7%g...@9.3.0~cxx~debug~fortran~hl~java+mpi+pic+shared~szip~threadsafe api=none arch=linux-centos7-sandybridge ^hy...@2.18.2%g...@9.3.0~complex~debug~int64~internal-superlu~mixedint+mpi~openmp+shared~superlu-dist patches=6e3336b1d62155f6350dfe42b0f9ea25d4fa0af60c7e540959139deb93a26059 arch=linux-centos7-sandybridge ^lib...@0.10.0%g...@9.3.0 arch=linux-centos7-sandybridge ^libffi@3.3%g...@9.3.0 patches=26f26c6f29a7ce9bf370ad3ab2610f99365b4bdd7b82e7c31df41a3370d685c0 arch=linux-centos7-sandybridge ^libi...@1.16%g...@9.3.0 arch=linux-centos7-sandybridge ^lib...@1.0.3%g...@9.3.0 arch=linux-centos7-sandybridge ^lib...@2.9.10%g...@9.3.0~python arch=linux-centos7-sandybridge ^me...@5.1.0%g...@9.3.0~gdb~int64~real64+shared build_type=Release patches=4991da938c1d3a1d3dea78e49bbebecba00273f98df2a656e38b83d55b281da1,b1225da886605ea558db7ac08dd8054742ea5afe5ed61ad4d0fe7a495b1270d2 arch=linux-centos7-sandybridge ^mu...@5.3.3%g...@9.3.0+complex+double+float~int64~metis+mpi~parmetis~ptscotch~scotch+shared arch=linux-centos7-sandybridge ^ncurses@6.2%g...@9.3.0~symlinks+termlib arch=linux-centos7-sandybridge ^netlib-s...@2.1.0%g...@9.3.0~ipo~pic+shared build_type=Release patches=1c9ce5fee1451a08c2de3cc87f446aeda0b818ebbce4ad0d980ddf2f2a0b2dc4,f2baedde688ffe4c20943c334f580eb298e04d6f35c86b90a1f4e8cb7ae344a2 arch=linux-centos7-sandybridge ^open...@0.3.12%g...@9.3.0~consistent_fpcsr~ilp64+pic+shared threads=none arch=linux-centos7-sandybridge ^ope...@3.1.6%g...@9.3.0~atomics~cuda~cxx~cxx_exceptions+gpfs~java~legacylaunchers~lustre~memchecker~pmi~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=none schedulers=none arch=linux-centos7-sandybridge ^ope...@1.1.1h%g...@9.3.0+systemcerts arch=linux-centos7-sandybridge ^parm...@4.0.3%g...@9.3.0~gdb~int64~ipo+shared build_type=RelWithDebInfo patches=4f892531eb0a807eb1b82e683a416d3e35154a455274cf9b162fb02054d11a5b,50ed2081bc939269689789942067c58b3e522c269269a430d5d34c00edbc5870,704b84f7c7444d4372cb59cca6e1209df4ef3b033bc4ee3cf50f369bce972a9d arch=linux-centos7-sandybridge ^pe...@5.32.0%g...@9.3.0+cpanm+shared+threads arch=linux-centos7-sandybridge ^pe...@3.11.4%g...@9.3.0~X~batch~cgns~complex~cuda~debug+double~exodusii~fftw~giflib+hdf5+hypre~int64~jpeg~knl~libpng~libyaml~memkind+metis~moab~mpfr+mpi+mumps~p4est~random123~saws+shared~suite-sparse+superlu-dist~trilinos~valgrind clanguage=C arch=linux-centos7-sandybridge ^pkg...@1.7.3%g...@9.3.0 arch=linux-centos7-sandybridge ^pyt...@3.8.6%g...@9.3.0+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib patches=0d98e93189bc278fbc37a50ed7f183bd8aaf249a8e1670a465f0db6bb4f8cf87 arch=linux-centos7-sandybridge ^readline@8.0%g...@9.3.0 arch=linux-centos7-sandybridge ^sql...@3.33.0%g...@9.3.0+column_metadata+fts~functions~rtree arch=linux-centos7-sandybridge ^superl...@6.1.1%g...@9.3.0~cuda~int64~ipo~openmp+shared build_type=RelWithDebInfo cuda_arch=none arch=linux-centos7-sandybridge ^t...@1.32%g...@9.3.0 arch=linux-centos7-sandybridge ^x...@5.2.5%g...@9.3.0~pic arch=linux-centos7-sandybridge ^zl...@1.2.11%g...@9.3.0+optimize+pic+shared arch=linux-centos7-sandybridge'
Lukasz Kaczmraczyk
Dec 1, 2021, 11:29:39 AM12/1/21
to MoFEM Q&A
Daniel, please try commands,
spack install -j2 --only dependencies mofem-cephas%gcc _AT_ 9.3.0 ^petsc+X ^openmpi _AT_ 3.1.6%gcc _AT_ 9.3.0 ^slepc~arpack
You can find it here,
Note: Instead of _AT_ use "@" and no spaces.
Lukasz
daniele.barbera86
Dec 1, 2021, 11:44:25 AM12/1/21
to MoFEM Q&A
I honestly did this before, while waiting for here I tried a solution I found on stack overflow and I did directly Spack install slepc, and once I run again the line of command you suggested it worked as a charm, now I am installing UM. Will keep you posted.
daniele.barbera86
Dec 1, 2021, 4:01:46 PM12/1/21
to MoFEM Q&A
Ok in the end I wiped the old installation and tried again, and it went better however when I have to install the User Modules using the developer guideline I got the same issue. I used this:
spack dev-build \
--source-path $HOME/mofem_install/mofem-cephas \
--keep-prefix \
--test root \
mofem-cephas@develop~copy_user_modules ^petsc+X
Still working on that to understand what is wrong, if anyone has a suggestion is really welcome :)
Lukasz Kaczmraczyk
Dec 2, 2021, 4:11:25 AM12/2/21
to MoFEM Q&A
Try this,
spack dev-build \
--source-path $HOME/mofem_install/mofem-cephas \
--keep-prefix \
--test root \
mofem-cephas@develop~copy_user_modules ^petsc+X ^ope...@3.1.6%g...@9.3.0 ^slepc~arpack
we have to specify that we going to use openmpi from cluster, and variant of slepc.
L.
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