[firedrake] Problem with installing FireDrake on cluster
Matthew Knepley
knepley at gmail.com
Wed Mar 10 20:48:22 GMT 2021
On Wed, Mar 10, 2021 at 3:15 PM Cynthia Cornelius <cdc at buffalo.edu> wrote:
> Dear Matt,
>
> Attached is the log file. Thank you.
>
Firedrake people, I see a few things:
1) The PETSc problem is a PTScotch problem. Barry fixed this, but I do not
know how to specify the PETSc version.
2) MPICH is being installed, but it should actually point to the cluster
MPICH
3) It seems like we should just install PETSc on the cluster with the right
packages. How should that work with installation?
Cynthia, I will send you a PETSc configure that is like the one I already
have, but with the Firedrake packages. We will build
it from the most recent snapshot to avoid the PTScotch problem.
Thanks,
Matt
> Best regards,
> Cynthia
>
> Cynthia Cornelius
> HPC Systems Analyst
> Center for Computational Research
> University at Buffalo
> ------------------------------
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* Wednesday, March 10, 2021 2:53 PM
> *To:* Cynthia Cornelius <cdc at buffalo.edu>
> *Cc:* firedrake at imperial.ac.uk <firedrake at imperial.ac.uk>
> *Subject:* Re: [firedrake] Problem with installing FireDrake on cluster
>
> On Wed, Mar 10, 2021 at 2:44 PM Cynthia Cornelius <cdc at buffalo.edu> wrote:
>
> Greetings,
>
> I'm trying to install Firedrake software on our cluster. I cannot use
> sudo nor apt-get. We have several users who would love to run this
> software on the cluster. Any suggestions that you may have will be most
> welcome.
>
>
> Hi Cynthia,
>
> Can you send
>
> /util/academic/firedrake/20210310-basic/firedrake-install.log
>
> Thanks,
>
> Matt
>
> Here are the error messages on the screen:
> Depending on your platform, PETSc may take an hour or more to build!
> Traceback (most recent call last):
> File "firedrake-install", line 1568, in <module>
> install("petsc/")
> File "firedrake-install", line 833, in install
> build_and_install_petsc()
> File "firedrake-install", line 959, in build_and_install_petsc
> check_call([python, "./configure", "PETSC_DIR={}".format(petsc_dir),
> "PETSC_ARCH={}".format(petsc_arch)] + list(petsc_
> options))
> File "firedrake-install", line 614, in check_call
> log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT,
> env=os.environ).decode())
> File
> "/util/academic/firedrake/20210310-basic/anaconda3/lib/python3.8/subprocess.py",
> line 411, in check_output
> return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
> File
> "/util/academic/firedrake/20210310-basic/anaconda3/lib/python3.8/subprocess.py",
> line 512, in run
> raise CalledProcessError(retcode, process.args,
> subprocess.CalledProcessError: Command
> '['/util/academic/firedrake/20210310-basic/firedrake/bin/python',
> './configure', 'P
> ETSC_DIR=/util/academic/firedrake/20210310-basic/firedrake/src/petsc',
> 'PETSC_ARCH=default', '--with-cxx-dialect=C++11', '
> --download-hwloc', '--with-shared-libraries=1', '--download-mumps',
> '--download-netcdf', '--download-scalapack', '--downlo
> ad-ptscotch', '--download-hypre', '--download-hdf5', '--download-ml',
> '--with-c2html=0', '--download-superlu_dist', '--wit
> h-debugging=0', '--download-pastix', '--download-metis',
> '--download-suitesparse', '--download-pnetcdf', '--with-zlib', '-
> -with-fortran-bindings=0',
> '--download-eigen=/util/academic/firedrake/20210310-basic/firedrake/src/eigen-3.3.3.tgz
> ', '--d
> ownload-chaco', '--download-mpich']' returned non-zero exit status 1.
> Install log saved in
> /util/academic/firedrake/20210310-basic/firedrake-install.log
>
>
> Here are the error messages from the firedrake-install.log:
> make[2]: Leaving directory
> `/util/academic/firedrake/20210310-basic/firedrake/src/petsc/default/externalpackages/git.ptscotc
>
> h/src/libscotch'
> make[1]: Leaving directory
> `/util/academic/firedrake/20210310-basic/firedrake/src/petsc/default/externalpackages/git.ptscotc
> h/src/libscotch'In file included from /usr/include/sys/wait.h:30:0,
> from common.h:130,
> from common_string.c:57:
> /petsc'
> 2021-03-10 13:37:20,781 DEBUG New path
> '/util/academic/firedrake/20210310-basic/firedrake/src'
> 2021-03-10 13:37:20,791 INFO
> Install log saved in
> /util/academic/firedrake/20210310-basic/firedrake-install.log
>
> Details of the environment for the build:
> cmake/3.17.1
>
> Anaconda Python 3.8
> [cdc at vortex2:/util/academic/firedrake/20210310-basic]$ python
> Python 3.8.5 (default, Sep 4 2020, 07:30:14)
> [GCC 7.3.0] :: Anaconda, Inc. on linux
> Type "help", "copyright", "credits" or "license" for more information.
> >>> quit()
>
> [cdc at vortex2:/util/academic/firedrake/20210310-basic]$ which gcc
> /usr/bin/gcc
> [cdc at vortex2:/util/academic/firedrake/20210310-basic]$ gcc --version
> gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
>
> [cdc at vortex2:/util/academic/firedrake/20210310-basic]$ cat
> /etc/redhat-release
> CentOS Linux release 7.9.2009 (Core)
> [cdc at vortex2:/util/academic/firedrake/20210310-basic]$ uname -a
> Linux srv-p22-13.cbls.ccr.buffalo.edu 3.10.0-1160.15.2.el7.x86_64 #1 SMP
> Wed Feb 3 15:06:38 UTC 2021 x86_64 x86_64 x86_64 GN
> U/Linux
>
> [cdc at vortex2:/util/academic/firedrake/20210310-basic]$ rpm -qf
> /usr/include/sys/wait.h
> glibc-headers-2.17-323.el7_9.x86_64
>
> Best regards,
> Cynthia
>
> Cynthia Cornelius
> HPC Systems Analyst
> Center for Computational Research
> University at Buffalo
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>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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