RE: AMBER: Blue Gene, compile Amber9?

From: Mike Hanby <>
Date: Tue, 10 Apr 2007 10:13:11 -0500

I'm attempting to use the PMEMD config.h from the scripps web site:


The compilation starts complaining on line 213 of the attached output
about "undefined refrence to `__ctype_b'


1501-510 Compilation successful for file erfcfun.f90.

blrts_xlf90 -o pmemd gbl_constants.o gbl_datatypes.o state_info.o
file_io_dat.o parallel_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o
prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o parallel.o pme_direct.o
pme_recip.o pme_fft.o fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o
cit.o dynamics.o bonds.o angles.o dihedrals.o runmd.o loadbal.o shake.o
runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o
timers.o pmemd_lib.o runfiles.o file_io.o bintraj.o pmemd_clib.o pmemd.o
random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o
master_setup.o alltasks_setup.o pme_setup.o ene_frc_splines.o
nextprmtop_section.o -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts
-lmsglayer.rts -lrts.rts -ldevices.rts -lm

/opt/ibmcmp/xlf/bg/10.1/blrts_lib/libxlf90.a(beginio.o): In function

c:(.text+0x23e): undefined reference to `__ctype_b'

c:(.text+0x103a): undefined reference to `__ctype_b'


I've attached the "make install 2>&1 |tee pmemd-make.log" output and my
config.h file


Does anyone have any suggestions?



From: [] On Behalf
Of Mike Hanby
Sent: Tuesday, April 10, 2007 09:04
Subject: RE: AMBER: Blue Gene, compile Amber9?


Thanks for the feedback Ross and Carlos, I'll compile just the PMEMD
component then. And thanks for the link to the SDSC page :-)



From: [] On Behalf
Of Ross Walker
Sent: Friday, April 06, 2007 16:24
Subject: RE: AMBER: Blue Gene, compile Amber9?


Dear Mike,


There is little point trying to run the rest of Amber on Blue Gene. The
scaling of sander is not sufficient to be efficient on Blue Gene and the
memory requirements will likely stop you running any decent size


PMEMD scales much better than sander and requires less memory. The
memory usage also goes down with the cpu count making it more suitable
for Blue Gene. Note PMEMD 9 supports both PME simulations and implicit
solvent GB simulations.


I attach the config.h I used to build pmemd 9 on SDSC's Blue Gene. Try
the one on the Amber website first though since this may have been
optimized by Bob Duke and give better performance. Benchmarks and job
submission scripts are here:


Note: Blue Gene is not a machine that was actively targetted by the
Amber developers during the Amber 9 development and so the code has not
had any specific optimizations for Blue Gene. Amber 10's PMEMD may
contain some Blue Gene tweaks that will improve the performance but this
won't be released until next year. Bob Duke may be able to comment more.


All the best


|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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        From: []
On Behalf Of Mike Hanby
        Sent: Friday, April 06, 2007 10:23
        Subject: AMBER: Blue Gene, compile Amber9?



        Has anyone compiled Amber9 for use on an IBM Blue Gene/L (bgl)
system that wouldn't mind sharing the steps they used to cross compile
the code using the blrts_xl compilers?


        I found one section on the Amber site that provides a config.h
file for compiling pmemd but nothing to do with the rest of Amber.


        Thanks, Mike

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Received on Wed Apr 11 2007 - 06:07:38 PDT
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