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

From: Harish Vashisth (harish.vashisth_at_gmail.com)
Date: Fri Jun 20 2014 - 18:49:59 CDT

Hi Axel:
sorry to bother you with this again.

  I have another quick question about your suggestions: When you say
executables have to be usually statically linked--I am wondering if there
is any way to include/link the shared object library during NAMD
installation from source.

In my situation, I have many tcl/C routines that i have combined using SWIG
into a shared library. i want access to these routines from tclforces
utility in NAMD. Would you have any suggestions as to how I may enable
access to such functions on CRAY without dynamically loading them.

Thanks a lot again.

-Harish

On Fri, Jun 20, 2014 at 3:36 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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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