[Clas_offline] compiling/running gsim on centos62

Thu Apr 4 04:17:39 EDT 2013

Sorry, the correct path to my files is:

/volatile/clas/claseg1dvcs/silvia/part_b/pi0/gsim/

Silvia

On Thu, 4 Apr 2013, Silvia Niccolai wrote:

> Hello Johann,
> thanks for your reply. Here are the results of my test.
> I logged into ifarm1102. But the environment script for tcsh gave me the
> following error:
>
> source /group/clas/builds/test3/environment.csh
> dirname: invalid option -- 't'
> Try `dirname --help' for more information.
>
> Just for trying, I ran gsim_bat after this error, but I got segmentation
> fault.
>
> So I moved to bash shell, and here the environment script gives no error.
> But when I tried to run gsim_bat, I got segmentation fault again.
>
> Here is my command line:
>
> /group/clas/builds/test3/bin/gsim_bat -ffread gsim_bat_eg1dvcs_b.ffread
> -mcin pi0_2000.bos -bosout pi0_2000_newgsim.gsim
>
> And here are the details of the the error message:
>
> GUSER_PHYS I: *** Default version of guser_phys called ***
> GUSER_BOOK I: *** Default version of guser_book called ***
> GUSER_BEG  I: *** Default version of guser_beg called ***
>
>  DZVERI --- UGINIT: check bank structure
> OPTIONS : CLFSU          OK
> file[ 0]->pi0_2000.bos<-
> bosClose : close local file
> bosClose : Call cclose(stream=1,iobptr=0,medium=2)
> -100
>
> Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
>
> Backtrace for this error:
> #0  0x7F87338E3E77
> #1  0x7F87338E4444
> #2  0x3345E328FF
> #3  0x3345E8CAB7
> #4  0x6529B9 in ctimef_
> #5  0x461CEE in gsimpar_2_bos_
> #6  0x40C201 in uginit_
> #7  0x40B2ED in MAIN__ at gsim_bat.F:0
> Segmentation fault
>
> I saw this kind of error before, and I actually found an email that I had
> sent three years ago to clas_offline, reporting the same error after
> compiling gsim on ifarml64. At that time I got no reply ;-), but I finally
> managed to compile it and have a working executable, playing with the
> various paths to libraries and scons options.
>
> So, maybe we could try this way: if you give me an environment script that
> works in tcsh (probably the error I get is a trivial one, but I am not
> familiar with this stuff) and the commands you used to compile the gsim
> packages and gsim_bat, I'll try to compile them myself.
>
> Maybe at the same time you could try run my same test on your machine
> with your executable, and see if you get my same error.
> My test input file in /volatile/clas/claseg1dvcs/gsim/pi0_2000.bos , and
> the ffread is in the same place,
> /volatile/clas/claseg1dvcs/gsim/gsim_bat_eg1dvcs_b.ffread .
> If you don't get errors, there are clearly issues only on my side, maybe
> some mixup in my environment.
>
> Thank you again for your help.
> best regards,
> Silvia
>
>
> On Wed, 3 Apr 2013, Johann Goetz wrote:
>
>> Hi Silvia,
>> Sorry it took so long to get back to you. It seems the problems you are
>> seeing come from the cernlibs. I have tested some very basic simulation
>> using gsim_bat but I would like you to verify that this works for you. I
>> put it into /group/clas/builds/test3 and you should source this environment
>> script before running anything:
>>
>> ssh ifarm1102        #  <-- this is the only rhel6 interactive node
>>
>> source /group/clas/builds/test3/environment.csh
>>
>> After this is done, you should see that gsim_bat is in your path and it
>> should be located here:
>> which gsim_bat
>> /group/clas/builds/test3/bin/gsim_bat
>>
>> Once you test it, I will move the environment script to what I hope to be
>> the "canonical" location of the CLAS run-time environment:
>> /group/clas/builds/environment.csh       # <-- for tcsh and csh
>> /group/clas/builds/environment.sh         # <-- for bash and sh
>>
>> But know that this will ONLY work on rhel6 systems and there is only one
>> interactive node: (ifarm1102). This should fail on ifarm1101 which is the
>> older rhel5 system.
>>
>>
>> -- Johann <https://sites.google.com/site/theodoregoetz/>
>>
>>
>> On Wed, Apr 3, 2013 at 8:36 AM, Silvia Niccolai <silvia at jlab.org> wrote:
>>
>>> Hello Dennis and Johann,
>>> last week I sent the email below to the clas_offline mailing list, but so
>>> far I had no reply. So I am retrying, sending it only to the two of you :-)
>>>
>>> I am quite concerned - but maybe it is just because I have no informations
>>> on the actual situation - about the transition of the farm to centos62. If
>>> all nodes are going to be replaced by the early fall (this is what I
>>> understood, I'll be glad if you correct me if I am wrong) we do need to
>>> have running executables for all the "standard" CLAS analysis and
>>> simulation codes, mainly GSIM, user_ana, and gpp.
>>>
>>> If this is not achievable, for reasons that are beyond my very little
>>> understanding of computing, compiling and the like, we should probably ask
>>> Computer Center not to replace all farm nodes, to leave things how they
>>> stand now or at least to leave enough nodes with the centos52 machines for
>>> us to be able to run jobs of CLAS6 analyses.
>>>
>>> I think this is an important issue that doesn't concern only my group
>>> (still heavily involved in CLAS6 analyses, with PhD students and post-docs,
>>> at different stages of advancement), but I presume most of the CLAS
>>> collaborators.
>>>
>>> Could you guys please give me an idea of the actual situation, and the
>>> next steps? Or, if there is actually no problems and the codes can be
>>> compiled fine, could you please tell me how to do that?
>>>
>>> Thank you very much and best regards,
>>>
>>> Silvia
>>>
>>>
>>> ---------- Forwarded message ----------
>>> Date: Thu, 28 Mar 2013 06:15:54 -0400 (EDT)
>>> From: Silvia Niccolai <silvia at jlab.org>
>>> To: clas_offline at jlab.org
>>> Subject: compiling/running gsim on centos62
>>>
>>> Hello, I have been trying to compile and run gsim on centos62, without
>>> success.
>>>
>>> I first tried the available executable in the "official" bin directory,
>>> but it crashes with a segmentation fault.
>>>
>>> I then checked out from svn the latest gsim and tried to compile it. The
>>> gsim packages compiles fine (both at 32 and at 64 bits), but errors arise
>>> when compiling gsim_int and gsim_bat. I tried at 32 bits first (problems of
>>> missing libraries, then once I found the right paths to the libraries there
>>> were errors related with gfortran...) and at 64 bits (all cernlib-related
>>> errors, which didn't go away no matter which available path to cernlibs at
>>> 64 bits I tried).
>>>
>>> As there is soon to be the migration of the farm to centos62, and several
>>> analyses of 6 GeV data are still ongoing, it would be really good if we
>>> could have some tips on how to produce working executables of all the
>>> "classic" 6-GeV codes (gsim, user_ana, gpp,...) on centos62.
>>>
>>> Every suggestion or offer for help is more than welcome.
>>>
>>> Thank you very much and best regards, Silvia
>>>
>>>
>>
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