From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Nov 26 2012 - 00:11:25 CST
Great, so have fun.
And don't forget to keep the list in cc.
~Norman
Von: flavio seixas [mailto:oivalf_nix_at_yahoo.com]
Gesendet: Freitag, 23. November 2012 15:17
An: Norman Geist
Betreff: Re: AW: AW: namd-l: libcudart.so.4 error
Hi Norman.
You are right!
My mistake! I am ashamed.
Sorry for de inconvenience.
Its working very fine now.
Flavio
--- On Fri, 11/23/12, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
From: Norman Geist <norman.geist_at_uni-greifswald.de>
Subject: AW: AW: namd-l: libcudart.so.4 error
To: "'flavio seixas'" <oivalf_nix_at_yahoo.com>
Cc: "Namd Mailing List" <namd-l_at_ks.uiuc.edu>
Date: Friday, November 23, 2012, 1:43 PM
You may not put files into the path variable, only folders. So putting the
folder of your namd installation to the start of your PATH, it should work.
This are linux basics and not related to NAMD.
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von flavio seixas
Gesendet: Freitag, 23. November 2012 11:48
An: 'Thomas Evangelidis'; Norman Geist
Cc: Namd Mailing List
Betreff: Re: AW: namd-l: libcudart.so.4 error
Hi.
Yes, it works, but only if I put libcudart.so.4 file at folder I running
namd.
Flavio
--- On Fri, 11/23/12, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
From: Norman Geist <norman.geist_at_uni-greifswald.de>
Subject: AW: namd-l: libcudart.so.4 error
To: "'Thomas Evangelidis'" <tevang3_at_gmail.com>
Cc: "Namd Mailing List" <namd-l_at_ks.uiuc.edu>
Date: Friday, November 23, 2012, 6:50 AM
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/
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