From: Michael Grabe (mgrabe_at_itsa.ucsf.edu)
Date: Tue Aug 23 2005 - 17:16:56 CDT
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
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