[molpro-user] Installation issues when installing for a cluster with a Myrinet network

[Evgeniy Gromov]

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:

cd /tmp/egromov/
long output file: 
/home/thor2/egromov/prog/molpro2006.1/pCMe_H2O_vert_6-31G.log
/opt/mpichgm-intel_NEW/bin/mpirun.ch_gm -np 1 --gm-kill 10 
/home/thor2/egromov/prog/molpro2006.1/bin/molprop_2006_1_i4_athlon_myrinet.exe
odin.cl1: Connection refused
status=256

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).

Best,
Evgeniy

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 
> -Wl,-rpath,/software/ACML-gnu64/lib/
> 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,
> 
> Kirk
> 
> 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,
>> Evgeniy
>>
>> Kirk Peterson wrote:
>>> Dear Evgeniy,
>>> I have a very similar cluster and in my case the various (myrinet) 
>>> CONFIG options are:
>>> WRAPPER="/opt/mpich/myrinet/gnu/bin/mpirun.ch_gm"
>>> MPI_LIB="/opt/mpich/myrinet/gnu/lib"
>>> MYRINET_LIB="/opt/gm/lib"
>>> MYRINET_LINKPARS="-lpthread -L/opt/mpich/myrinet/gnu/lib -lmpich 
>>> -L/opt/gm/lib -lgm"
>>> LIBDIR_myrinet=/home/kipeters/ga-4-0/lib/LINUX
>>> WRAPPER_myrinet=/opt/mpich/myrinet/gnu/bin/mpirun.ch_gm
>>> 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.
>>> regards,
>>> Kirk
>>> 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:
>>>>
>>>> WRAPPER=.../ga-4-0-1/tcgmsg/ipcv4.0/parallel
>>>> LIBDIR_tcgmsg=/home/thor2/egromov/prog/ga-4-0-1/lib/LINUX
>>>> WRAPPER_tcgmsg=/usr/local/ga-4-0/tcgmsg/ipcv4.0/parallel
>>>>
>>>> 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,
>>>> Evgeniy
>>>>
>>>> --_______________________________________
>>>> Dr. Evgeniy Gromov
>>>> Theoretische Chemie
>>>> Physikalisch-Chemisches Institut
>>>> Im Neuenheimer Feld 229
>>>> D-69120 Heidelberg
>>>> Germany
>>>>
>>>> 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
>> Germany
>>
>> 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
Germany

Telefon: +49/(0)6221/545263
Fax: +49/(0)6221/545221
E-mail: evgeniy at pci.uni-heidelberg.de
_______________________________________