VMD-L Mailing List

From: Marc Baaden (baaden_at_smplinux.de)
Date: Mon Mar 13 2006 - 07:29:36 CST

Hi,

we have some trouble making IMD work between a visualisation/interaction
client running VMD under Linux and a NAMD calculation on an IBM SP4. I
wonder whether anybody has successfully used such a combination? The
underlying question is whether there is a specific problem with our setup
or a general problem with these architectures.

For more details see below (a yet unanswered detailed description sent to
the NAMD mailing list by a colleague).

Thank you very much in advance,
  Marc Baaden

Subject: Problem to run IMD simulation
From: Laurent Leger <Laurent.Leger_at_idris.fr>
Date: Fri, 24 Feb 2006 11:29:29 +0100

Hi All,

I'm trying to run an IMD simulation with VMD (1.8.4b6 for Linux workstation)
and with NAMD (2.6b1 for IBM-SP) but without success.

I downloaded the binaries of each software on the respective web sites.

My problem is that I'm not able to connect two softwares on a TCP/IP port.

My chosen IP port (54321) isn't a restricted port and I have no restriction
to access to the IBM SP4 from the Linux workstation.

So I don't see where the problem is.

I have made somes investigations :
 a/ I tried to connect VMD (on the same Linux wokstation) with NAMD on a SGI
    computer (Onyx 3800). I had no problem : IMD simulation runs perfectly.

    So I thought that 1.8.4b6 version of VMD for Linux is OK and I looked on
    the side of NAMD on my IBM SP4.

 b/ In first, I saw that NAMD didn't listen on TCP/IP port even if I have
    theses lines in my config file :
        IMDon yes
        IMDport 54321
        IMDfreq 1
        IMDwait on

    I have found a workaround by setting "++server-port" flag of NAMD.
    That seems strange to me to have to use this flag. I have the same
    problem if I run NAMD under LoadLeveler control or directly from the
    prompt. Does anyone have the same problem with an IBM-SP host ?

 c/ So now, I run NAMD on my IBM SP4 with the command :
        namd ++server-port 54321 config-file

    Like this, I have a unix process listenning on 54321 IP port. Then, when
    I run VMD (on Linux workstation), I can see a connection established
    between two hosts on this IP port. But VMD returns this error message :

        ERROR) Unable to ascertain relative endianness of remote machine
        Unable to connect to host zahir on port 54321

    The connection is immediatly closed (because VMD is unable to ascertain
    endianness). But, on IBM-SP, the IP port has the CLOSE_WAIT status (thus
    something has been exchanged between two hosts on IP port).
    In more, NAMD doesn't detect the connection and stay in wait mode. It's
    seem to me that NAMD is unable to use the IP port.

      Does anyone can explain me this problem ?

For information, I specifie that my IBM SP4 uses 64 bits adressing mode and
downloaded binaries are designed to run in 32 bits adressing mode.

  Is the reason of my problem ?

I tried to built my own version of NAMD by setting "-q64" flag of xlC compiler.
But builted executable doesn't run. I have a "Memory fault" message.

  Is there someone who compile NAMD with 64 bit adressing mode ?

Have you an idea to help me ?

Thanks for your help.

        Laurent Leger 

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden_at_smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217