[petsc-users] Question about PETSc installs and MPI

[Francis Poulin]

Hello Barry,

I was one of the two people that had difficulties with getting the correct results with John's code.  Previously, I didn't have valgrind installed so I installed it using apt-get.  Then I configured it using the following:

./configure --with-scalar-type=complex --with-cc=gcc -—with-cxx=c++ --with-fc=gfortran --with-c2html=0 --download-mpich --download-scalapack --download-hypre

This is on ubuntu and is different from what I tried before in that now I am downloading mpich, scalapack and hypre.   I decided to download scalapack since that seems like it could be useful.  I was told that HYPRE doesn't work with complex variables.  Too bad, but not a big deal.

It completes the configure, make all and make test and even gives me the figures of the parallel efficiency (or not quite efficiency maybe).  I didn't catch any errors, but there are possible errors in the log.  When I went to try making an example I found that I can't use petscmpiexec to run anything in serial or parallel.

fpoulin at vortex:~/software/petsc/src/ts/examples/tutorials$ /home/fpoulin/software/petsc/bin/petscmpiexec -n 1 ./ex1
-bash: /home/fpoulin/software/petsc/bin/petscmpiexec: /bin/csh: bad interpreter: No such file or directory

I am sorry to bother you with this.  I am also having issues with my installation on my mac but I thought if i can figure this one out then maybe I will have a better idea what's wrong with the other.

Thank,
Francis


------------------
Francis Poulin
Associate Professor
Associate Chair, Undergraduate Studies
Department of Applied Mathematics
University of Waterloo

email:           fpoulin at uwaterloo.ca
Web:            https://uwaterloo.ca/poulin-research-group/
Telephone:  +1 519 888 4567 x32637


________________________________________
From: Barry Smith [bsmith at mcs.anl.gov]
Sent: Friday, July 18, 2014 9:57 PM
To: John Yawney
Cc: petsc-users at mcs.anl.gov; Francis Poulin; Kim Usi
Subject: Re: [petsc-users] Question about PETSc installs and MPI

   I ran the program on linux with 1,2, 4 processes under valgrind for both types of boundary conditions and it ran fine.

   Suggest your colleagues do a test configure of PETSc using —download-mpich and see if they still get the problem or if it runs ok.

   The can also run with valgrind and see what it reports. http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind

   Barry

On Jul 18, 2014, at 8:16 PM, John Yawney <jyawney123 at gmail.com> wrote:

> Hello,
>
> I had a question about PETSc installations. On my local computer I configured PETSc (v 3.4.2) using the options:
>
> ./configure --with-cc=mpicc --with-cxx=mpic++ --download-f-blas-lapack --download-mpich --download-hypre
>
> I wrote a test program that defines a vector using DMDAs, computes a dot product, exchanges halo elements, and computes a low-order FD derivative of the vector. Under my installation of PETSc everything works fine. For some reason, when my colleagues run the program, they get segmentation fault errors. If they change the y and z boundary types to GHOSTED as well, they get the program to run until the end (seg faults at the end though) but they get a local value of the dot product. I've attached the main.cpp file for this script.
>
> When they installed their versions of PETSc they didn't use the --download-mpich option but instead used either:
> ./configure --download-f-blas-lapack --with-scalar-type=complex
> or with the option: --with-mpi-dir=/home/kim/anaconda/pkgs/mpich2-1.3-py27_0
>
> Could this be causing a problem with the parallelization under PETSc?
>
> Thanks for the help and sorry for the long question.
>
> Best regards,
> John
> <main.cpp>

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