[Mvapich-discuss] [mvapich-discuss] MVAPICH2 2.3.5 and HDF5 1.10.7 parallel tests

[Subramoni, Hari]

Hi, Mark.

Please accept my sincere apologies for the delay here.

Unfortunately, we have not got around to looking into this yet. We will look into it over the next couple of days and get back to you.

Best,
Hari.

PS: I've CC'ed the e-mail to the new address for MVAPICH-Discuss 

-----Original Message-----
From: Mark Dixon <mark.c.dixon at durham.ac.uk> 
Sent: Thursday, February 11, 2021 4:23 AM
To: Subramoni, Hari <subramoni.1 at osu.edu>
Cc: mvapich-discuss at cse.ohio-state.edu <mvapich-discuss at mailman.cse.ohio-state.edu>
Subject: RE: [mvapich-discuss] MVAPICH2 2.3.5 and HDF5 1.10.7 parallel tests

(Resending, as this doesn't appear in the list archives so may have been lost in the move of the mailing list....)

Hi all,

Has anyone had the time to take a look at this and run my script demonstrating this problem with MPI-IO / HDF5, please?

I've verified this as an issue on the two platforms I've tested:

- rhel 7 / POWER9 / Lustre
- centos 7 / Intel / ext4

Thanks,

Mark


On Tue, 15 Dec 2020, Mark Dixon wrote:

> Hi Hari,
>
> Thanks for replying. Just tried it out on an x86 box with Truescale 
> IB, running centos7.8 - same result.
>
> This time, files were on an ext4 filesystem and no lustre was 
> available (so compiled with "--enable-romio --with-file-system=ufs")
>
> Best,
>
> Mark
>
> On Tue, 15 Dec 2020, Subramoni, Hari wrote:
>
>>
>>  [EXTERNAL EMAIL] Do not open links or attachments unless you 
>> recognise the  sender and know the content is safe. Otherwise, use 
>> the Report Message  button or report to phishing at durham.ac.uk<"mailto:phishing at durham.ac.uk>.
>>
>>  Hi, Mark.
>>
>>  Sorry to hear that you're facing issues.
>>
>>  Can you please let us know if the is issue particular to POWER9 + 
>> Lustre +  UFS combination or does it happen on x86 systems as well?
>>
>>  We will try out the steps you've mentioned locally and see if we are 
>> able  to reproduce it.
>>
>>  Thx,,
>>  Hari.
>>
>>  -----Original Message-----
>>  From: mvapich-discuss-bounces at cse.ohio-state.edu
>>  <mvapich-discuss-bounces at mailman.cse.ohio-state.edu> On Behalf Of 
>> Mark  Dixon
>>  Sent: Tuesday, December 15, 2020 12:11 PM
>>  To: mvapich-discuss at cse.ohio-state.edu
>>  <mvapich-discuss at mailman.cse.ohio-state.edu>
>>  Subject: [mvapich-discuss] MVAPICH2 2.3.5 and HDF5 1.10.7 parallel 
>> tests
>>
>>  Hi there,
>>
>>  I'm having trouble getting HDF5's parallel tests to pass when built 
>> on top  of MVAPICH2. I was wondering if anyone else is seeing this, please?
>>
>>  For reference (not sure it's relevant), I had similar trouble with 
>> the  version of ROMIO bundled inside OpenMPI  
>> (https://urldefense.com/v3/__https://github.com/open-mpi/ompi/issues/
>> 6871__;!!KGKeukY!nWOQssfAxiSnSZJJ7bf62O6vhk438EzOmw7yXziKQ3niAaJZUYlm
>> w-6k6nKp0Si8pwjiqKIs-3I4CJc$
>>  )
>>
>>  Thanks,
>>
>>  Mark
>> 
>>
>>  #!/bin/bash
>> 
>> #  We have run this on an IBM POWER9 rhel7.6-alt system with MOFED 
>> 4.7. The #  # hdf5 test "testphdf5" does not complete until it is 
>> terminated by (in #  # this case) a 1 hour alarm timeout.
>> #
>> #  The last lines that the test printed was 6 copies of this:
>> #
>> # Testing  -- multi-chunk collective chunk io (cchunk3) # # This has 
>> been # run from a location on an xfs filesystem, and # on a lustre 
>> filesystem, # with the same result.
>>
>>  set -x
>>  set -e
>>
>>  # (needed on our system to ensure we are using the OS-provided # 
>> version  of GCC, etc.) module purge || true
>>
>>  test -d build || mkdir build
>>  test -d src || mkdir src
>>
>>  prefix=`pwd`/build
>>  export PATH=${prefix}/bin:$PATH
>>
>>  cd src
>> 
>>
>>  # mvapich2
>>
>>  wget
>>  
>> https://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3.
>> 5.tar.gz
>>  tar xf mvapich2-2.3.5.tar.gz
>>  (
>>     cd mvapich2-2.3.5
>>
>>     ./configure --prefix=$prefix \
>>         --enable-romio \
>>         --with-file-system=lustre+ufs
>>
>>     make -j12
>>     make install
>> )
>> 
>>
>>  # hdf5
>>
>>  wget
>>  
>> https://urldefense.com/v3/__https://support.hdfgroup.org/ftp/HDF5/rel
>> eases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7.tar.gz__;!!KGKeukY!nWOQss
>> fAxiSnSZJJ7bf62O6vhk438EzOmw7yXziKQ3niAaJZUYlmw-6k6nKp0Si8pwjiqKIsvYU
>> 7Edc$
>>  tar xf hdf5-1.10.7.tar.gz
>>  (
>>     cd hdf5-1.10.7
>>
>>     export CC=mpicc
>>     export CXX=mpicxx
>>     export FC=mpif90
>>     export F77=mpif77
>>     export F90=mpif90
>>
>>     export HDF5_ALARM_SECONDS=3600
>>
>>     ./configure --prefix=$prefix --enable-parallel
>>     make -j12
>>     make check
>>     make install
>> )
>>
>>  _______________________________________________
>>  mvapich-discuss mailing list
>>  mvapich-discuss at cse.ohio-state.edu
>>  http://mailman.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss
>> 
>