[ExM Users] turbine call does not return when invoking from Galaxy

[Ketan Maheshwari]

It is 3.0.2:

$ mpiexec -version
HYDRA build details:
    Version:                                 3.0.2
    Release Date:                            Wed Jan 30 17:38:15 CST 2013
    CC:                              gcc
    CXX:                             c++
    F77:                             gfortran
    F90:                             gfortran
    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'
    Process Manager:                         pmi
    Launchers available:                     ssh rsh fork slurm ll lsf sge
manual persist
    Topology libraries available:            hwloc
    Resource management kernels available:   user slurm ll lsf sge pbs
    Checkpointing libraries available:       blcr
    Demux engines available:                 poll select

==========

$ mpicc -v
mpicc for MPICH version 3.0.2
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.6/lto-wrapper
Target: x86_64-linux-gnu
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
Thread model: posix
gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)





On Fri, May 9, 2014 at 12:29 PM, Wozniak, Justin M. <wozniak at mcs.anl.gov>wrote:

>
> Can you tell us which MPI you are using?  We will have to address this...
>
>
> On 05/09/2014 10:08 AM, Tim Armstrong wrote:
>
> Nice!
>
>
> On Fri, May 9, 2014 at 9:30 AM, Ketan Maheshwari <ketan at mcs.anl.gov>wrote:
>
>> Hi Mike,
>>
>>  Thanks! Redirecting stdin from /dev/null with turbine call worked right
>> away!
>>
>>  So, now  we have a first working version of Swift/T-foreach-Galaxy.
>>
>>  Thanks,
>> Ketan
>>
>>
>>  On Thu, May 8, 2014 at 8:33 PM, Wilde, Michael J. <wilde at mcs.anl.gov>wrote:
>>
>>>  Perhaps try redirecting stdin on the $turbine call with "< /dev/null"
>>>
>>> Some older versions of mpiexec had a bug when stdin was not a tty or
>>> ptty.
>>>
>>> Not sure if thats the case here, but easy to try.
>>>
>>> - Mike
>>>
>>>
>>> On 5/8/14, 5:10 PM, Ketan Maheshwari wrote:
>>>
>>>   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
>>>
>>>
>>>
>>>
>>>    _______________________________________________
>>> ExM-user mailing listExM-user at lists.mcs.anl.govhttps://lists.mcs.anl.gov/mailman/listinfo/exm-user
>>>
>>>
>>> --
>>> Michael Wilde
>>> Mathematics and Computer Science          Computation Institute
>>> Argonne National Laboratory               The University of Chicago
>>>
>>>
>>
>> _______________________________________________
>> ExM-user mailing list
>> ExM-user at lists.mcs.anl.gov
>> https://lists.mcs.anl.gov/mailman/listinfo/exm-user
>>
>>
>
>
> _______________________________________________
> ExM-user mailing listExM-user at lists.mcs.anl.govhttps://lists.mcs.anl.gov/mailman/listinfo/exm-user
>
>
>
> --
> Justin M Wozniak
>
>
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