[molpro-user] Installing molpro - GA toolkit needed, or can we use openmpi by itself (solved)

[Benji Wakely]

Thanks Andy,

tar -tzvf molpro.2010.1.23.tar.gz |grep -e abdata.ascii -e rysrw.ascii
  -rw-r--r-- wwwrun/www  4440906 2011-06-25 04:12:57 Molpro/lib/rysrw.ascii
  -rw-r--r-- wwwrun/www   782386 2011-06-25 04:12:56 Molpro/lib/abdata.ascii
The files were there in the source.

Thanks for your help and patience in diagnosing what now seems to be not-a-molpro related problem.



I have now successfully compiled and installed molpro using:
(pgi 11.8) + (openmpi compiled against pgi 11.8) + (torque v.2.5.5)
(intel 12.0) + (openmpi compiled against intel 12.0) + (torque v.2.5.5)



Testing compilation between different nodes in our cluster
pointed towards the node doing the compilation being the problem.
(It worked on a different node in the cluster. 
 Same setup, same environment modules...)

Unfortunately I didn't manage to narrow down the exact cause of the problem.
If I find anything definitively wrong with the node, I'll be happy 
to share...


Thanks again for your time.

--Benji

Benji Wakely - b.wakely at latrobe.edu.au
Unix Systems Administrator

Work phone: +613 9479 5499
mobile: +614 34 307 667


>-----Original Message-----
>From: mayaj1 at Cardiff.ac.uk [mailto:mayaj1 at Cardiff.ac.uk]
>Sent: Wednesday, 7 September 2011 11:19 PM
>To: Benji Wakely
>Cc: molpro-user at molpro.net
>Subject: Re: [molpro-user] Installing molpro - GA toolkit needed, or can
>we use openmpi by itself?
>
>Benji,
>
>This error is very strange and indicates some of the Molpro source files
>are missing, can you confirm that 'abdata.ascii' is actually present?
>The tarball certainly contains these:
>
>~/test> tar -xzf ~/molpro.2010.1.23.tar.gz
>~/test> ls Molpro/lib/*.ascii
>Molpro/lib/abdata.ascii  Molpro/lib/rysrw.ascii
>
>It's worth also checking the file permissions, but I don't see how only
>these files could have somehow changed since the rest of the source
>files are obviously readable for you to be able to compile them.
>
>Can you try generating the auxiliary files ABDATA and RYSRW again by:
>
>rm -f lib/{ABDATA,RYSRW,init.log}
>make	
>
>and once again check the contents of lib/init.log.
>
>Best wishes,
>
>Andy
>
>On 07/09/11 04:55, Benji Wakely wrote:
>> Output of lib/init.log:
>>
>> ----------------
>> cat lib/init.log
>>
>>   ? Error
>>   ? The abdata.ascii file does not exist
>>   ? The problem occurs in cnvrt
>> <error type="Error" location="cnvrt" message="The abdata.ascii file
>does not exist"/>
>> [hercules005:28469] *** Process received signal ***
>> [hercules005:28469] Signal: Segmentation fault (11)
>> [hercules005:28469] Signal code: Address not mapped (1)
>> [hercules005:28469] Failing at address: (nil)
>> [hercules005:28469] *** End of error message ***
>> ----------------------------------------------------------------------
>----
>> mpirun noticed that process rank 0 with PID 28469 on node
>hercules005.latrobe.edu.au exited on signal 11 (Segmentation fault).
>> ----------------------------------------------------------------------
>----
>> ----------------
>>
>> I can invoke mpirun with a simple mpi script,
>> (Not running on the head node), and it seems to work correctly.
>>
>> (For what it's worth, openmpi was compiled with:
>>   CC=pgcc CXX=pgcpp F77=pgf77 FC=pgf90 ./configure --
>prefix=/usr/local/openmpi/1.4.3-pgi --with-openib --with-
>tm=/usr/local/torque/latest --enable-static --enable-shared
>> )
>>
>> (the 'with-tm' is torque v.2.5.5)
>>
>>
>> Here's a verbose listing of the process I'm using to compile/make
>molpro,
>> for public scrutiny/possible embarrassment:
>>
>> # set up basic molpro files
>> - set up ~/.molpro/token
>> - extract molpro source file (molpro.2010.1.23.tar.gz)
>>
>> # set up PGI compilers
>> - ensure PGI version 11.8 binaries are in PATH
>> - ensure LD_LIBRARY_PATH includes PGI 'lib' and 'libso' directories
>>
>> # set up openmpi (openmpi compiled against PGI 11.8)
>> - ensure CPPFLAGS references openmpi 'include' directory
>> - ensure LDFLAGS references openmpi 'lib' directory
>> - ensure MPI_DIR and MPI_HOME reference openmpi base directory
>> - ensure LD_LIBRARY_PATH includes openmpi 'lib' directory
>>
>> # configure molpro
>> export TMPDIR=/tmp
>> CONFIGURE_OPTIONS="-openmpi -pgf90 -pgcc -blaspath
>/usr/local/pgi/linux86-64/11.8/lib -mpp -mppbase
>/usr/local/openmpi/1.4.3-pgi/include -var
>INSTBIN=/usr/local/molpro/2010.1-openmpi-pgi/bin -var
>INSTLIB=/usr/local/molpro/2010.1-openmpi-pgi/lib -var
>INSTHTML=/usr/local/molpro/2010.1-openmpi-pgi/html"
>> ./configure -batch $CONFIGURE_OPTIONS
>>
>> make -j8
>>
>> ...I can't spot anything I'm doing that's obviously wrong.
>>
>> --Benji
>>
>> Benji Wakely - b.wakely at latrobe.edu.au
>> Unix Systems Administrator
>>
>> Work phone: +613 9479 5499
>> mobile: +614 34 307 667
>>
>>
>>> -----Original Message-----
>>> From: mayaj1 at Cardiff.ac.uk [mailto:mayaj1 at Cardiff.ac.uk]
>>> Sent: Tuesday, 6 September 2011 11:18 PM
>>> To: Benji Wakely
>>> Cc: molpro-user at molpro.net
>>> Subject: Re: [molpro-user] Installing molpro - GA toolkit needed, or
>can
>>> we use openmpi by itself?
>>>
>>> Benji,
>>>
>>> I see nothing obviously wrong with your CONFIG file, I've just tested
>>> building a copy of Molpro with pretty much the same versions of
>>> compilers, libraries etc. as you, and it works fine.
>>>
>>> The problem you saw is that the auxiliary file ABDATA is not present.
>>> This file (and others) are created at 'make' time by running an
>>> initialization job. Can you check the contents of lib/init.log which
>>> should have the output from running that job? It looks as though your
>>> openmpi build has been configured with some special options to
>interact
>>> with the queue system, does this prevent the use of mpirun on the
>>> (head?) node where you are building?
>>>
>>> Best wishes,
>>>
>>> Andy
>>>
>>> On 06/09/11 00:37, Benji Wakely wrote:
>>>> Hi Andy, thanks for the response.
>>>>
>>>> 1)
>>>> When you say 'MPI2', this includes the openmpi implementation of
>MPI2,
>>> yes?
>>>> (openmpi doesn't use mpd as such - but mpiexec seems to be working,
>>>>    which I believe means it's working.  Corrections welcomed!)
>>>>
>>>> I've attached the generated CONFIG file from the PGI attempt.
>>>>
>>>> I can provide the output from the compilation process if the CONFIG
>>> file doesn't help.
>>>>
>>>> Best,
>>>> --Benji
>>>>
>>>> Benji Wakely - b.wakely at latrobe.edu.au
>>>> Unix Systems Administrator
>>>>
>>>> Work phone: +613 9479 5499
>>>> mobile: +614 34 307 667