[molpro-user] Installation issues when installing for a cluster with a Myrinet network
Evgeniy.Gromov at pci.uni-heidelberg.de
Fri May 9 17:40:14 BST 2008
Dear Kirk and Gerald Knizia
Thanks a lot for your responses. Indeed some lapack and blas libraries
were missing on the cluster nodes and I had to set up additional
ld_library paths. But unfortunately this had not solved the problem -
it doesn't run anyway. Maybe I do (or did) something wrong, but when
I run it with -v option (i.e. molpro -v) it gives:
long output file:
/opt/mpichgm-intel_NEW/bin/mpirun.ch_gm -np 1 --gm-kill 10
odin.cl1: Connection refused
and then stops.
Does it look reasonable until "odin.cl1: Connection refused"? What
this "odin.cl1: Connection refused" with "status=256" means I have no
idea. Likely that is the problem. Note that I get this when running
just on one node interactively (the node has 2 processors).
Gerald Knizia wrote:
> You may need to include additional dynamic libraries either in the rpath when
> linking the executable or to the environment variable LD_LIBRARY_PATH. Both
> are ways to tell the dynamic linker where to find .so libraries. You can
> find out which exactly need to be found by using
> ldd molpro.exe
> In the output of this command, each .so required should point to a concrete
> file on the file system with that name. You can include this command in your
> submit-script and inspect the output in order to see which are the missing
> libraries when molpro is executed by the queing engine.
> In the case where some external launcher (like "parallel") is required, you
> may also need to make sure that this one can be executed (try to run it and
> see if the OS complains).
> Examples for a library specification with rpath (in this case for the ACML
> math library, you will most likely need other libraries! Which that are is
> what ldd can tell you.):
> BLASLIB=-L/software/ACML-gnu64/lib/ -lacml -lacml_mv -lg2c
> Here the -L tells the static linker where to find the .lib files, and the
> Wl,-rpath tells it to embed the actual directories into the executable, so
> that the dynamic linker (which is run when the program is) can find them.
> Such linker flags are specified at link time (i.e., when you build molpro)
> Example for LD_LIBRARY_PATH:
> bash: export LD_LIBRARY_PATH=/software/ACML-gnu64/lib/:$LD_LIBRARY_PATH
> csh: setenv LD_LIBRARY_PATH /software/ACML-gnu64/lib/:$LD_LIBRARY_PATH
> these need to be specified before molpro is run. (i.e., in some shell-script
> that is run before molpro is invoked).
Kirk Peterson wrote:
> Dear Evgeniy,
> what output do you get when you start molpro with "molpro -v" ? You
> could also
> turn on verbose output in mpirun.ch_gm as well (also giving a -v on its
> command line).
> best regards,
> On May 9, 2008, at 6:07 AM, Evgeniy Gromov wrote:
>> Dear Kirk,
>> Many thanks for your help! I made the settings
>> in my CONFIG similar to yours and managed to compile
>> the code. However now I am again in troubles as
>> I cannot run any test. It looks like the executable
>> is dead or cannot start as the output and errout
>> files are empty. Did you have something like that
>> when installing the code. Thanks!
>> Best regards,
>> Kirk Peterson wrote:
>>> Dear Evgeniy,
>>> I have a very similar cluster and in my case the various (myrinet)
>>> CONFIG options are:
>>> MYRINET_LINKPARS="-lpthread -L/opt/mpich/myrinet/gnu/lib -lmpich
>>> -L/opt/gm/lib -lgm"
>>> of course the location of mpirun.ch_gm (/opt/mpich/myrinet/gnu/bin in
>>> m case) should be in your path.
>>> If this doesn't work for you, let me know and I can send my whole
>>> CONFIG file to you.
>>> On May 8, 2008, at 6:13 AM, Evgeniy Gromov wrote:
>>>> Dear molpro aficionados!
>>>> I am attempting to install Molpro2006.1 in a parallel
>>>> mode on a athlon cluster with a Myrinet network. I have
>>>> installed GA with the GM Myricom library. When running
>>>> configure, it prompts to choose among tcgmsg, mpi or myrinet.
>>>> It is said in the manual that if myrinet network is available
>>>> "myrinet" should be choosen. My question is what should be set
>>>> then in the CONFIG file for: WRAPPER=, LIBDIR_myrinet= and
>>>> WRAPPER_myrinet= ?
>>>> On the other hand if I choose tcgmsg then:
>>>> Is this right?
>>>> But when compiling I immediately get an error message from make:
>>>> GNUmakefile:56: *** Cannot find 'parallel' command in PATH. Stop.
>>>> I will very appreciate if someone could clarify (help to resolve) these
>>>> two issues!
>>>> Best wishes,
>>>> Dr. Evgeniy Gromov
>>>> Theoretische Chemie
>>>> Physikalisch-Chemisches Institut
>>>> Im Neuenheimer Feld 229
>>>> D-69120 Heidelberg
>>>> Telefon: +49/(0)6221/545263
>>>> Fax: +49/(0)6221/545221
>>>> E-mail: evgeniy at pci.uni-heidelberg.de
>> Dr. Evgeniy Gromov
>> Theoretische Chemie
>> Physikalisch-Chemisches Institut
>> Im Neuenheimer Feld 229
>> D-69120 Heidelberg
>> Telefon: +49/(0)6221/545263
>> Fax: +49/(0)6221/545221
>> E-mail: evgeniy at pci.uni-heidelberg.de
Dr. Evgeniy Gromov
Im Neuenheimer Feld 229
E-mail: evgeniy at pci.uni-heidelberg.de
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