From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Nov 23 2012 - 00:50:54 CST
Hi,
the latest answer should work. Additionally, if you will run parallel jobs
with charmrun, you should look at the ++runscript option.
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Thomas Evangelidis
Gesendet: Donnerstag, 22. November 2012 22:33
An: namd-l
Betreff: Re: namd-l: libcudart.so.4 error
This may be your problem:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/vmd/libcudart.so.4
You append the libcudart.so.4 path at the end of $LD_LIBRARY_PATH and NAMD
uses the first instance it finds (the ones that you previously appended).
Try this one this time:
export LD_LIBRARY_PATH=$NAMD_HOME:$LD_LIBRARY_PATH
~Thomas
On 22 November 2012 23:17, Aron Broom <broomsday_at_gmail.com> wrote:
So you got it working by putting the library that ships with NAMD in the
folder? If so, then it should be more or less what you started with, in
that you should set your LD_LIBRARY_PATH to include the folder holding the
decompressed NAMD binaries and the library.
Test that and see if it works, maybe the ones you were linking to before
just weren't formatted the way NAMD expected and so it returned an error
saying it couldn't find it or something.
~Aron
On Thu, Nov 22, 2012 at 3:26 PM, flavio seixas <oivalf_nix_at_yahoo.com> wrote:
Hi,
I tryed to copy namd2 and executables (including libcudart.so.4 file) to
/usr/bin/ folder in order to every user can access.
No way.
Namd2 works only when libcudart.so.4 is placed in every folder I run namd.
Any suggestion to make libcudart.so.4 as startable?
regards,
Flavio
--- On Thu, 11/22/12, Thomas Evangelidis <tevang3_at_gmail.com> wrote:
From: Thomas Evangelidis <tevang3_at_gmail.com>
Subject: Re: namd-l: libcudart.so.4 error
To: "namd-l" <namd-l_at_ks.uiuc.edu>
Date: Thursday, November 22, 2012, 7:50 PM
Try also running:
./namd2 +setcpuaffinity +p2 +idlepoll +devices 0 input.conf
~Thomas
On 22 November 2012 21:25, Aron Broom <broomsday_at_gmail.com
<http://mc/compose?to=broomsday@gmail.com> > wrote:
Why didn't your locate find the library that comes with NAMD? In general
that is the one you should give it, not sure that will solve your problems
though.
~Aron
On Thu, Nov 22, 2012 at 1:42 PM, flavio seixas <oivalf_nix_at_yahoo.com
<http://mc/compose?to=oivalf_nix@yahoo.com> > wrote:
Hi, I am trying to run namd2 with cuda in a dualcore fedora14 x64, cuda
capable Nvidia GeForce GT430.
I found the following error:
[root_at_perseus]# locate libcudart.so.4
/usr/bin/libcudart.so.4
/usr/local/lib/vmd/libcudart.so.4
/usr/local/vmd-1.9.1/lib/redistrib/lib_LINUXAMD64/libcudart.so.4
/usr/sbin/libcudart.so.4
[root_at_perseus]#
[root_at_perseus]# export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/vmd/libcudart.so.4
[root_at_perseus]# ./namd2 +idlepoll +p2 input.conf > output.log &
[1] 4379
[root_at_perseus]# ./namd2: error while loading shared libraries:
libcudart.so.4: cannot open shared object file: No such file or directory
[1]+ Exit 127 ./namd2 +idlepoll +p2 input.conf > output.log
[root_at_perseus]#
Could someone tells me what is missing?
Thanks for any help.
Flavio
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang_at_pharm.uoa.gr <http://mc/compose?to=tevang@pharm.uoa.gr> tevang3_at_gmail.com <http://mc/compose?to=tevang3@gmail.com> website: https://sites.google.com/site/thomasevangelidishomepage/ -- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang_at_pharm.uoa.gr tevang3_at_gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:17 CST