From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Aug 25 2005 - 18:36:34 CDT
Yes, all of your nodes must have access to libibmc++.A.dylib. The easy
way to accomplish this is to copy libibmc++.A.dylib to some directory and
then setenv DYLD_LIBRARY_PATH /that/directory in your .cshrc file.
-Jim
On Tue, 23 Aug 2005, Michael Grabe wrote:
> hi namd list,
>
> i just installed the NAMD 2.6b1 precompiled binary
> on my MAC OSX server and I then downloaded the
> IBM compilers.
>
> I can get NAMD 2.6b1 to run in standalone mode,
> and I can get my old NAMD2.5 install to run in
> parrellel. But I get the following error when I try to run NAMD 2.6b1
> on many computers in parallel. Do all of my nodes have
> to have access to the /opt/ibmcmp/lib/libibmc++.A.dylib library?
> Because right now only my head node does.
>
> Thank you in advance, and here is my error at the command prompt:
>
> Timeout waiting for node-program to connect
>
> And from the ++verbose I get:
>
> Charmrun rsh(mrgreen.7)> rsh phase successful.
> Charmrun rsh(mrswhite.6)> rsh phase successful.
> Charmrun rsh(mrgreen.3)> rsh phase successful.
> Charmrun> adding client 0: "profplum", IP:XXX.XXX.XX.20
> Charmrun> adding client 1: "colmustard", IP:XXX.XXX.XX.21
> Charmrun> adding client 2: "mrswhite", IP:XXX.XXX.XX.22
> Charmrun> adding client 3: "mrgreen", IP:XXX.XXX.XX.23
> Charmrun> adding client 4: "profplum", IP:XXX.XXX.XX.20
> Charmrun> adding client 5: "colmustard", IP:XXX.XXX.XX.21
> Charmrun> adding client 6: "mrswhite", IP:XXX.XXX.XX.22
> Charmrun> adding client 7: "mrgreen", IP:XXX.XXX.XX.23
> Charmrun> Charmrun = XXX.XXX.XX.20, port = 59796
> Charmrun> Sending "0 XXX.XXX.XX.20 59796 10408 0" to client 0.
> Charmrun> find the node program "/downloads/NAMD_2.6b1/namd2" at
> "/Volumes/Big_Plum1/Users/mgrabe/Projects/mac_osx_test" for 0.
> Charmrun> Starting ssh profplum -l mgrabe /bin/sh -f
> Charmrun> Sending "1 XXX.XXX.XX.20 59796 10408 0" to client 1.
> Charmrun> find the node program "/downloads/NAMD_2.6b1/namd2" at
> "/Users/mgrabe/Projects/mac_osx_test" for 1.
> Charmrun> Starting ssh colmustard -l mgrabe /bin/sh -f
> Charmrun> Sending "2 XXX.XXX.XX.20 59796 10408 0" to client 2.
> Charmrun> find the node program "/downloads/NAMD_2.6b1/namd2" at
> "/Users/mgrabe/Projects/mac_osx_test" for 2.
> Charmrun> Starting ssh mrswhite -l mgrabe /bin/sh -f
> Charmrun> Sending "3 XXX.XXX.XX.20 59796 10408 0" to client 3.
> Charmrun> find the node program "/downloads/NAMD_2.6b1/namd2" at
> "/Users/mgrabe/Projects/mac_osx_test" for 3.
> Charmrun> Starting ssh mrgreen -l mgrabe /bin/sh -f
> Charmrun> Sending "4 XXX.XXX.XX.20 59796 10408 0" to client 4.
> Charmrun> find the node program "/downloads/NAMD_2.6b1/namd2" at
> "/Volumes/Big_Plum1/Users/mgrabe/Projects/mac_osx_test" for 4.
> Charmrun> Starting ssh profplum -l mgrabe /bin/sh -f
> Charmrun> Sending "5 XXX.XXX.XX.20 59796 10408 0" to client 5.
> Charmrun> find the node program "/downloads/NAMD_2.6b1/namd2" at
> "/Users/mgrabe/Projects/mac_osx_test" for 5.
> Charmrun> Starting ssh colmustard -l mgrabe /bin/sh -f
> Charmrun> Sending "6 XXX.XXX.XX.20 59796 10408 0" to client 6.
> Charmrun> find the node program "/downloads/NAMD_2.6b1/namd2" at
> "/Users/mgrabe/Projects/mac_osx_test" for 6.
> Charmrun> Starting ssh mrswhite -l mgrabe /bin/sh -f
> Charmrun> Sending "7 XXX.XXX.XX.20 59796 10408 0" to client 7.
> Charmrun> find the node program "/downloads/NAMD_2.6b1/namd2" at
> "/Users/mgrabe/Projects/mac_osx_test" for 7.
> Charmrun> Starting ssh mrgreen -l mgrabe /bin/sh -f
> Charmrun> waiting for rsh (profplum:0), pid 10409
> Charmrun> waiting for rsh (colmustard:1), pid 10410
> Charmrun> waiting for rsh (mrswhite:2), pid 10411
> Charmrun> waiting for rsh (mrgreen:3), pid 10412
> Charmrun> waiting for rsh (profplum:4), pid 10413
> Charmrun> waiting for rsh (colmustard:5), pid 10414
> Charmrun> waiting for rsh (mrswhite:6), pid 10415
> Charmrun> waiting for rsh (mrgreen:7), pid 10416
> Charmrun> Waiting for 0-th client to connect.
> Charmrun> client 0 connected (IP=XXX.XXX.XX.20 data_port=49971)
> Charmrun> Waiting for 1-th client to connect.
> Charmrun> client 4 connected (IP=XXX.XXX.XX.20 data_port=49972)
> Charmrun> Waiting for 2-th client to connect.
>
> -michael
> --------------------------------------------------------------------------------------------------
> Michael Grabe, Ph.D.
> HHMI/UCSF
> Genetics Development & Behavioral Science Building
> 1550 4th Street, GD 482
> San Francisco, CA 94143-0725
> tel: ++ 415.476.0421
> http://itsa.ucsf.edu/~mgrabe
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:05 CST