[Swift-user] Re: [beagle-users] [SWIFT on Beagle]Cannot Execute Correctly After Submitting Job

[Weiyang Wang]

OK Thanks.

I'm working on the makefile now, shall we meet tomorrow afternoon?

On Wed, Apr 27, 2011 at 5:00 AM, Lorenzo Pesce <lpesce at uchicago.edu> wrote:

> Weiyang,
>
> Can you wait until tomorrow morning? I have to run off campus right now and
> I do not have the time to give you a complete reply.
> I should be able to look into your problem before noon or so.
>
>
> Lorenzo
>
> On Apr 26, 2011, at 2:14 PM, Weiyang Wang wrote:
>
> OK, I've "make clean" them and  ow I switched to PrgEnv-cray, and going to
> use ftn to compile some .for files, although they are currently not
> recognizable by ftn. I want them to be compiled as F90 files (maybe I have
> to rename them first? )
>
> Could you kindly check out what's going on here within the makefile?
>
>
> ======= the first several lines====
> OBJDIR = objCSMINPUT
> FC     = ftn
> FFLAGS = -O 3 -g
> INC    = -I.
> MKDIR  = mkdir -p
> DIRS   = ../Common ../Input
> RM     = rm -rf
> ===========================
>
> ===somewhere it starts compiling===
>
> # Create a list of all source files including folder name
> FSRC   = $(foreach dir,$(DIRS),$(wildcard $(dir)/*.for))
>
> ## Create the list of all object files
> TOBJ   = $(foreach dir, $(DIRS), $(subst .for,.o,$(notdir $(wildcard
> $(dir)/*.for))))
>
> # Create the path to store the object files
> FOBJ   = $(foreach obj,$(TOBJ),$(OBJDIR)/$(obj))
>
> # Define the subfolders to look for source files
> vpath %.for ../Common ../Input
>
> $(OBJDIR)/%.o $(OBJDIR)/%.mod: %.for | $(OBJDIR)
>         $(FC) $(FFLAGS) $(INC) -o $@ -c $<
>
> ../MINPT040.EXE : $(FOBJ)
>         $(FC) $^ -o $@
>
>
> ============================
>
>
>
>
> On Wed, Apr 27, 2011 at 2:43 AM, Ketan Maheshwari <ketan at mcs.anl.gov>wrote:
>
>> Hello,
>>
>> This indicates that the executable is not running on beagle compute nodes.
>> Could you kindly send the commandline and the path to your exe, data etc,
>> and I can try to do some testing using aprun and qsub.
>>
>> Ketan
>>
>>
>> On Apr 26, 2011, at 1:26 PM, Weiyang Wang wrote:
>>
>> In fact I switched to PrgEnv-gnu to compile it again on Beagle, and it
>> works if I run it plainly on login.beagle
>>
>> On Tue, Apr 26, 2011 at 10:53 PM, Ti Leggett <leggett at ci.uchicago.edu>wrote:
>>
>>> -----BEGIN PGP SIGNED MESSAGE-----
>>> Hash: SHA1
>>>
>>> Was the code you're trying to run compiled on Beagle. IT looks to me like
>>> it was compiled on PADS. You must recompile your code on Beagle using the
>>> Cray compiler wrappers. Please refer to the Beagle FAQ on how to do this:
>>>
>>> http://www.ci.uchicago.edu/wiki/bin/view/Beagle/DevelopOnBeagle
>>>
>>> On Apr 26, 2011, at 9:34 AM, Weiyang Wang wrote:
>>>
>>> > Hello,
>>> >
>>> > I've meet problems when submitting jobs using Swift.
>>> >
>>> > My Command Line is like:
>>> >
>>> > swift -sites.file ./mysites.xml  -tc.file ./tc.data largescale.swift
>>> >
>>> > My mysites.xml is like
>>> > <config>
>>> > <pool handle="pbs">
>>> >     <execution provider="pbs" url="none" jobManager="local:pbs"/>
>>> >     <profile namespace="globus" key="maxwalltime">0:20:00</profile>
>>> >     <profile namespace="globus" key="workersPerNode">8</profile>
>>> >     <profile namespace="globus" key="ppn">8</profile>
>>> >     <!-- <profile namespace="globus"
>>> key="internalHostname">172.5.86.6</profile>-->
>>> >     <profile namespace="globus" key="nodeGranularity">1</profile>
>>> >     <profile namespace="globus" key="maxNodes">5</profile>
>>> >     <profile namespace="karajan" key="jobThrottle">1.99</profile>
>>> >     <profile namespace="karajan" key="initialScore">10000</profile>
>>> >     <profile namespace="globus" key="project">CI-SES000031</profile>
>>> >     <!--gridftp  url="local://localhost" />-->
>>> >     <filesystem provider="local"/>
>>> >     <!--scratch>/home/frankwang/tmp</scratch>-->
>>> >
>>> <workdirectory>/gpfs/pads/projects/CI-SES000031/csm/tempswiftwork</workdirectory>
>>> > </pool>
>>> > </config>
>>> >
>>> > My tc.data is like,
>>> > pbs             echo    /bin/echo       INSTALLED       INTEL32::LINUX
>>>  null
>>> > pbs             sh      /bin/bash       INSTALLED       INTEL32::LINUX
>>>  null
>>> >
>>> >
>>> > In my swift script I'm running some gfortran compiled programs(I wrap
>>> my fortran programs in sh files), and in my error log file, it shows that
>>> >
>>> > /gpfs/pads/projects/CI-SES000031/csm/DSSAT040.EXE: error while loading
>>> shared libraries: libgfortran.so.3: cannot open shared object file: No such
>>> file or directory
>>> >
>>> > I didn't meet the same problem when I run these on PADS, and after I
>>> swap the module to PrgEnv-gnu when logging onto Beagle I can also run this
>>> DSSAT040.EXE.
>>> > My guess is,  I submit the jobs to a Non-GNU Environment in Beagle.
>>> >
>>> > How can I correct this?
>>> >
>>> > Thank you.
>>> >
>>> > Weiyang
>>> > _______________________________________________
>>> > beagle-users mailing list
>>> > beagle-users at ci.uchicago.edu
>>> > http://mail.ci.uchicago.edu/mailman/listinfo/beagle-users
>>>
>>> -----BEGIN PGP SIGNATURE-----
>>> Version: GnuPG/MacGPG2 v2.0.14 (Darwin)
>>>
>>> iEYEARECAAYFAk223FkACgkQ4RgdOxQVi0AVxgCeNmnQ0e2xgmIZjQ3vkot1SpWf
>>> H5MAnjS/VbEaH7vWSJFcSK+2hs1VHo4d
>>> =8FUi
>>> -----END PGP SIGNATURE-----
>>>
>>
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>>
>>
>>
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