Nevermind. A coworker helped me figure this one out. Echo is treating
the '-E' as an argument to echo and interpreting it instead of passing
it to sed. Since that's used by the configure tests, that's a bit of a
problem, Just adding another -E before $@, should fix the problem.
Prentice
On 04/03/2017 03:54 PM, Prentice Bisbal wrote:
I've decided to work around this problem by creating a wrapper script
for pgcc that strips away the -pthread argument, but my sed expression
works on the command-line, but not in the script. I'm essentially
reproducing the workaround from
https://www.open-mpi.org/community/lists/users/2009/04/8724.php.
Can anyone see what's wrong with my implementation the workaround?
It's a very simple sed expression. Here's my script:
#!/bin/bash
realcmd=/path/to/pgcc
echo "original args: $@"
newargs=$(echo "$@" | sed s/-pthread//)
echo "new args: $newargs"
#$realcmd $newargs
exit
And here's what happens when I run it:
/path/to/pgcc -E conftest.c
original args: -E conftest.c
new args: conftest.c
As you can see, the -E argument is getting lost in translation. If I
add more arguments, it works fine:
/path/to/pgcc -A -B -C -D -E conftest.c
original args: -A -B -C -D -E conftest.c
new args: -A -B -C -D -E conftest.c
It only seems to be a problem when -E is the first argument:
$ /path/to/pgcc -E -D -C -B -A conftest.c
original args: -E -D -C -B -A conftest.c
new args: -D -C -B -A conftest.c
Prentice
On 04/03/2017 02:24 PM, Aaron Knister wrote:
To be thorough couldn't one replace -pthread in the slurm .la files
with -lpthread? I ran into this last week and this was the solution I
was thinking about implementing. Having said that, I can't think of a
situation in which the -pthread/-lpthread argument would be required
other than linking against statically compiled SLURM libraries and
even then I'm not so sure about that.
-Aaron
On 4/3/17 1:46 PM, Åke Sandgren wrote:
We build slurm with GCC, drop the -pthread arg in the .la files, and
have never seen any problems related to that. And we do build quite a
lot of code. And lots of versions of OpenMPI with multiple different
compilers (and versions).
On 04/03/2017 04:51 PM, Prentice Bisbal wrote:
This is the second suggestion to rebuild Slurm
The other from Åke Sandgren, who recommended this:
This usually comes from slurm, so we always do
perl -pi -e 's/-pthread//' /lap/slurm/${version}/lib/libpmi.la
/lap/slurm/${version}/lib/libslurm.la
when installing a new slurm version. Thus no need for a fakepg
wrapper.
I don't really have the luxury to rebuild Slurm at the moment. How
would
I rebuild Slurm to change this behavior? Is rebuilding Slurm with PGI
the only option to fix this in slurm, or use Åke's suggestion above?
If I did use Åke's suggestion above, how would that affect the
operation
of Slurm, or future builds of OpenMPI and any other software that
might
rely on Slurm, particulary with regards to building those apps with
non-PGI compilers?
Prentice
On 04/03/2017 10:31 AM, Gilles Gouaillardet wrote:
Hi,
The -pthread flag is likely pulled by libtool from the slurm
libmpi.la
<http://libmpi.la> and/or libslurm.la <http://libslurm.la>
Workarounds are
- rebuild slurm with PGI
- remove the .la files (*.so and/or *.a are enough)
- wrap the PGI compiler to ignore the -pthread option
Hope this helps
Gilles
On Monday, April 3, 2017, Prentice Bisbal <pbis...@pppl.gov
<mailto:pbis...@pppl.gov>> wrote:
Greeting Open MPI users! After being off this list for several
years, I'm back! And I need help:
I'm trying to compile OpenMPI 1.10.3 with the PGI compilers,
version 17.3. I'm using the following configure options:
./configure \
--prefix=/usr/pppl/pgi/17.3-pkgs/openmpi-1.10.3 \
--disable-silent-rules \
--enable-shared \
--enable-static \
--enable-mpi-thread-multiple \
--with-pmi=/usr/pppl/slurm/15.08.8 \
--with-hwloc \
--with-verbs \
--with-slurm \
--with-psm \
CC=pgcc \
CFLAGS="-tp x64 -fast" \
CXX=pgc++ \
CXXFLAGS="-tp x64 -fast" \
FC=pgfortran \
FCFLAGS="-tp x64 -fast" \
2>&1 | tee configure.log
Which leads to this error from libtool during make:
pgcc-Error-Unknown switch: -pthread
I've searched the archives, which ultimately lead to this work
around from 2009:
https://www.open-mpi.org/community/lists/users/2009/04/8724.php
<https://www.open-mpi.org/community/lists/users/2009/04/8724.php>
Interestingly, I participated in the discussion that lead to that
workaround, stating that I had no problem compiling Open MPI with
PGI v9. I'm assuming the problem now is that I'm specifying
--enable-mpi-thread-multiple, which I'm doing because a user
requested that feature.
It's been exactly 8 years and 2 days since that workaround was
posted to the list. Please tell me a better way of dealing with
this issue than writing a 'fakepgf90' script. Any suggestions?
--
Prentice
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