Re: NAMD on CRAY XE6m-200: dynamic linking in tcl not working

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jun 20 2014 - 14:36:37 CDT

On Fri, Jun 20, 2014 at 3:07 PM, Harish Vashisth
<harish.vashisth_at_gmail.com> wrote:
> Dear NAMD Users and Developers:
>
> We have recently installed NAMD2.9 from source on our CRAY machine (Machine
> configuration given here:
> http://trillian-use.sr.unh.edu/index.php/Main_Page.) Regular NAMD jobs are
> working fine, however, we are not able to load shared object files using
> "load" command under NAMD config. file. For example, making use of a

your cray machine is not a conventional linux cluster, but an MPP
machine with a specially modified kernel on the compute nodes that has
many features from standard kernels removed for optimal performance.
the ability to use the dlopen() function call and shared libraries on
the compute nodes in general is not enabled by default. please talk to
your system administrator and/or cray support expert. usually
executables have to be linked statically, but it may be possible on
newer cray runtime environments to re-enable dlopen() (likely with an
associated performance penalty).

axel.

> tclforces script like this; this is the simplest possible example we have
> tried which was created using tcl/swig.
>
> ###################################
> puts " loading shared object"
> load ./example.so example
> set ans [pow 3 4]
> puts "ANS: $ans "
> puts "Shared object working"
>
> proc calcforces { } {
> print "inside calcforces"
> }
> ################################
>
>
> The error we get when jobs crash is: dynamic loading is not currently
> available on this system.
>
>
> Looking here (http://wiki.tcl.tk/9830), we found that it is likely due to
> unavailability of a functional load command.
>
> Not sure if we missed anything imp. during installation?
>
> Previously on other Linux clusters, we have been able to successfully use
> above example and it works fine on a local workstation as well. Even on
> CRAY, loading the example.so under "tclsh" from terminal works fine.
>
>
> Here are some more details on two different ways we have tried installing
> NAMD, and both gave same dynamic loading not available error:
>
>
> [Not all of these modules are needed]
>
> module switch PrgEnv-cray PrgEnv-gnu
> module load rca
> module load craype-hugepages8M
> module load ugni
> module add gni-headers
> module add csa
>
> Charm++ from prior build:
> ./build charm++ gemini_gni-crayxe smp --with-production -j16
>
> From current build:
> env MPICXX=mpicxx \
> ./build charm++ mpi-crayxe smp -j32 --with-production
>
> NAMD
> config line from prior build:
> ./config CRAY-XT-g++ --charm-arch gemini_gni-crayxe-smp
>
> From current build:
> ./config CRAY-XT-g++ --charm-arch mpi-crayxe-smp
>
>
>
> Jobs are run using following command in a PBS script:
>
> aprun -n ${NUMPROCS} -cc none
> /home/rcc/rea/NAMD_2.9_Source/CRAY-XT-g++/namd2 $CONFFILE >& $LOGFILE
>
>
>
> Any help/suggestions are appreciated. Thanks.
>
>
>
>
>
>
> -----------------------
> Harish Vashisth
> Assistant Professor
> Department of Chemical Engineering
> University of New Hampshire, Durham, NH 03824
> Phone: (603)-862-2483
> ----------------------------------------------
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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