<div dir="ltr"><div>It is 3.0.2:<br><br>$ mpiexec -version<br>HYDRA build details:<br> Version: 3.0.2<br> Release Date: Wed Jan 30 17:38:15 CST 2013<br> CC: gcc<br>
CXX: c++<br> F77: gfortran<br> F90: gfortran<br> Configure options: '--disable-option-checking' '--prefix=/home/ketan/mpich3-install' '--enable-shared' '--cache-file=/dev/null' '--srcdir=.' 'CC=gcc' 'CFLAGS= -O2' 'LDFLAGS= ' 'LIBS=-lrt -lpthread ' 'CPPFLAGS= -I/homes/ketan/mpich-3.0.2/src/mpl/include -I/homes/ketan/mpich-3.0.2/src/mpl/include -I/homes/ketan/mpich-3.0.2/src/openpa/src -I/homes/ketan/mpich-3.0.2/src/openpa/src -I/homes/ketan/mpich-3.0.2/src/mpi/romio/include'<br>
Process Manager: pmi<br> Launchers available: ssh rsh fork slurm ll lsf sge manual persist<br> Topology libraries available: hwloc<br> Resource management kernels available: user slurm ll lsf sge pbs<br>
Checkpointing libraries available: blcr<br> Demux engines available: poll select<br><br>==========<br><br>$ mpicc -v<br>mpicc for MPICH version 3.0.2<br>Using built-in specs.<br>COLLECT_GCC=gcc<br>
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.6/lto-wrapper<br>Target: x86_64-linux-gnu<br>Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.6 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --enable-objc-gc --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu<br>
Thread model: posix<br>gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)<br><br><br><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, May 9, 2014 at 12:29 PM, Wozniak, Justin M. <span dir="ltr"><<a href="mailto:wozniak@mcs.anl.gov" target="_blank">wozniak@mcs.anl.gov</a>></span> wrote:<br>
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Can you tell us which MPI you are using? We will have to address this...<div class=""><br>
<br>
On 05/09/2014 10:08 AM, Tim Armstrong wrote:<br>
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<div dir="ltr">Nice!<br>
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<div class="gmail_quote"><div class="">On Fri, May 9, 2014 at 9:30 AM, Ketan Maheshwari <span dir="ltr">
<<a href="mailto:ketan@mcs.anl.gov" target="_blank">ketan@mcs.anl.gov</a>></span> wrote:<br>
</div><div><div class="h5"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Mike,
<div><br>
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<div>Thanks! Redirecting stdin from /dev/null with turbine call worked right away!</div>
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<div>So, now we have a first working version of Swift/T-foreach-Galaxy. </div>
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<div>Thanks,</div>
<div>Ketan</div>
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<div class="gmail_extra"><br>
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<div class="gmail_quote">
<div>On Thu, May 8, 2014 at 8:33 PM, Wilde, Michael J. <span dir="ltr"><<a href="mailto:wilde@mcs.anl.gov" target="_blank">wilde@mcs.anl.gov</a>></span> wrote:<br>
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<div>Perhaps try redirecting stdin on the $turbine call with "< /dev/null"<br>
<br>
Some older versions of mpiexec had a bug when stdin was not a tty or ptty.<br>
<br>
Not sure if thats the case here, but easy to try.<br>
<br>
- Mike
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<div>On 5/8/14, 5:10 PM, Ketan Maheshwari wrote:<br>
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<pre>Hi,
Trying invoke turbine from Galaxy as follows:
$turbine -V -n $n $wdir/script.tcl "${swiftargs}"
Each of the variables being set in previous lines.
The process tree shows mpiexec as defunct processes:
PID TTY TIME CMD
389 ? 00:00:00 sshd
390 pts/39 00:00:00 bash
804 pts/39 00:00:00 sh
990 pts/39 00:00:38 python
1189 pts/39 00:00:00 sh
1190 pts/39 00:00:00 bash
1330 pts/39 00:00:00 turbine
1332 pts/39 00:00:00 mpiexec <defunct>
1547 pts/39 00:00:00 sh
1548 pts/39 00:00:00 bash
1683 pts/39 00:00:00 turbine
1686 pts/39 00:00:00 mpiexec <defunct>
2046 pts/39 00:00:00 sh
2047 pts/39 00:00:00 bash
2299 pts/39 00:00:00 turbine
2302 pts/39 00:00:00 mpiexec <defunct>
Not sure how to debug this. The same call works outside of Galaxy.
Any suggestions?
Thanks,
Ketan
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<pre cols="72">--
Michael Wilde
Mathematics and Computer Science Computation Institute
Argonne National Laboratory The University of Chicago
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<pre cols="72">--
Justin M Wozniak</pre>
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