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

Benji Wakely B.Wakely at latrobe.edu.au
Wed Sep 7 04:55:43 BST 2011

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 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?
>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,
>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,
>> (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

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