[firedrake] Problem with installing FireDrake on cluster

Wed Mar 10 20:15:50 GMT 2021

Dear Matt,

  Attached is the log file.  Thank you.

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<mailto: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<http://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/>
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