From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Thu Nov 22 2012 - 15:33:10 CST
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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