Re: Namd-I: namd compiling problem

From: Ye Yang (knightyangpku_at_gmail.com)
Date: Wed Aug 03 2011 - 10:46:13 CDT

Hi, Norman:
Thanks for the advice.
The problem is that I did not use the cuda version, I just downloaded source
code and compiled it with multicore-linux64
, and it works perfectly on another machine.

Also, I have run namd (the linux64 version) on this machine, and it never
shows any problem with rsh before.

Is there anything that I could do?
Thank you very much.

Ye

2011/8/3 Norman Geist <norman.geist_at_uni-greifswald.de>

> Hi Ye,****
>
> ** **
>
> just follow the messages namd gives to you. When you want ro run parallel
> jobs, you need a program to logon to the other hosts, or even at single host
> runs, the host needs to connect to itself. Usually this is done with the
> command ssh (secure shell) or rsh (remote shell), both work fine. You need
> to have this tool installed on your machines you want to run namd on. This
> is usually very easy. ****
>
> ** **
>
> The other issue you have is the cuda version of namd. This version always
> needs to be runned with the +idlepoll parameter like:****
>
> ** **
>
> charmrun +p2 namd2 +idlepoll <yourconfig>****
>
> ** **
>
> AND your need to put your namd2 directory to the LD_LIBRARY_PATH to tell
> namd where to search for the libcudart, which is usually shipped with the
> downloadable binaries or maybe in the cuda toolkit or with your namdsource. This is done for example if your shell is bash:
> ****
>
> ** **
>
> export LD_LIBRARY_PATH=/your/namd-dir-with-the-lib/:$LD_LIBRARY_PATH****
>
> ** **
>
> This exports the environment variable with the right directory to the
> libcudart. If you want to run namd-cuda in parallel this is no problem on
> a single host. Just add ++local to the charmrun command to pas through the
> LD_LIBRARY_PATH to the other processes getting spawned. To run on multiblemachines you have to add the parameter ++
> runscript to the charm command to execute a script which exports the
> LD_LIBRARY_PATH on the target hosts before namd gets started, because you
> may not use the ++local command with runs on multible machines. The
> runsscript could look like:****
>
> ** **
>
> #!/bin/bash****
>
> export LD_LIBRARY_PATH=/your/namd-dir-with-the-lib/:$LD_LIBRARY_PATH****
>
> ** **
>
> Save it to runscript.sh for example and call namd like****
>
> ** **
>
> charmrun ++runscript runscript.sh +p4 ++nodelist yournodelist namd2 +
> idlepoll <yourconfig>****
>
> ** **
>
> Mit freundlichen Grüßen****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Ye Yang
> *Gesendet:* Mittwoch, 3. August 2011 05:28
> *An:* NAMD list
> *Betreff:* namd-l: Namd-I: namd compiling problem****
>
> ** **
>
> Dear namd experts:
>
> It seems that I have met some troubles when compiling namd.
> I am using the ./configure Linux-86_64-g++ charm-arch
> multicore-Linux64 to configure on two different machines..
> One of them is fine with "make", and runs normally.
> The other one, however shows some errors each time I run namd:
> error while loading shared libraries: libcudart.so.2: cannot open shared
> object file: No such file or directory. It makes me puzzled since I did not
> use the cuda version.
> when I use "find / -namd" to locate it, the result is:
> /usr/local/lib/vmd/libcudart.so.2
> Also, even if I I added the LD path to avoid this, there is still
> problem:
> when I try namd2, it always said "Please add +idlepoll to command
> line for proper performance"
> And if I try charmrun + p6 namd2, it will show:
> Charmrun> Couldn't find rsh program 'rsh'!
> Charmrun> Couldn't find rsh program 'rsh'!
> Charmrun> Error 1 returned from rsh (localhost:0)
> Charmrun> Couldn't find rsh program 'rsh'!
> Charmrun> Couldn't find rsh program 'rsh'!
> Could anyone help me with this?
> Thank you very much.
>
> Best
> Wishes
>
> Ye Yang
>
> ****
>

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