From: Rene Salmon (rsalmon_at_tulane.edu)
Date: Wed Apr 19 2006 - 13:34:16 CDT
Hi List,
We are having problems getting NAMD 2.6b1 on IBM Power5 using AIX
5.2 to run. I followed the instructions on the wiki
http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdOnAIX
and managed to compile both namd and charm. The problem we are still
having is that when we try to run NAMD using loadleveler and poe namd
just hangs after running for a few seconds and does nothing I am hopping
someone here can shed some light. Here is what I did to compile:
- Download nightly charm++
- ./build charm++ mpi-sp -qtune=pwr5 -O3 -qarch=pwr5 -DCMK_OPTIMIZE=1
This went fine no problems or error messages.
- In the NAMD source, in the file vmdsock.C, change:
SOCKLEN_T to NAMD_SOCKLEN_T, two occurences
- Here is what my AIX-POWER-xlC.arch make file looks like:
rsalmon_at_l2f1n01 73> cat AIX-POWER-xlC.arch
NAMD_ARCH = AIX-POWER
CHARMARCH = mpi-sp
CXX = xlC_r -w -qstaticinline -DMEMUSAGE_USE_SBRK
CXXOPTS = -O3 -qstrict -qaggrcopy=nooverlap -qalias=addr:ansi:typ -Q
-qarch=com -qtune=pwr5 -qfloat=rsqrt:fltint -bmaxdata:0x80000000
CXXNOALIASOPTS = -O3 -qaggrcopy=nooverlap -qalias=addr:allp:ansi:typ -Q
-qarch=com -qtune=pwr5 -qfloat=rsqrt:fltint -bmaxdata:0x80000000
CC = xlc_r -w
COPTS = -O4 -qinlglue -qarch=com -qtune=pwr5 -bmaxdata:0x80000000
- I also downloaded the pre-compiled tcl and fft libs and used this line
to config nand:
./config tcl fftw AIX-POWER-MPI-xlC
- Last I did a make and everything compiled fine no error messages.
- To run in loadleveler this is the command we are trying out:
>>/usr/bin/poe ~/NAMD_BIN/namd2 ++debug ~/namd-test/dyn1.conf
-So far the namd exec gets this far and then just hangs there forever:
Info: 0 IMPROPER
Info: 0 VDW
Info: 231 VDW_PAIRS
Warning: Man, tiny Elvis, that number is huge!
Warning: We don't know how X-Plor represents over Z999 residues
Warning: And you just tried [000 - so we'll fake it as 36000
Warning: This is reversible, but only inside this program.
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 134335 ATOMS
Info: 134744 BONDS
Info: 41064 ANGLES
Info: 74516 DIHEDRALS
Info: 0 IMPROPERS
Info: 232133 EXCLUSIONS
Info: 121866 RIGID BONDS
Info: 281139 DEGREES OF FREEDOM
Info: 49841 HYDROGEN GROUPS
Info: TOTAL MASS = 859916 amu
Info: TOTAL CHARGE = -3.92245e-05 e
Info: *****************************
Info: Entering startup phase 0 with 90742 kB of memory in use.
Info: Entering startup phase 1 with 90742 kB of memory in use.
Info: Entering startup phase 2 with 104184 kB of memory in use.
Info: Entering startup phase 3 with 104184 kB of memory in use.
Info: PATCH GRID IS 7 (PERIODIC) BY 7 (PERIODIC) BY 5 (PERIODIC)
Info: REMOVING COM VELOCITY -0.00777089 -0.00641697 -0.00793082
Info: LARGEST PATCH (130) HAS 628 ATOMS
Any ideas or clues on getting this to work?
Thank you
Rene
--
-
--
Rene Salmon
Tulane University
Center for Computational Science
Richardson Building 310
New Orleans, LA 70118
http://www.ccs.tulane.edu
Tel 504-862-8393
Fax 504-862-8392
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