Is there a general agreement on which is the better approach?
I have a user who wants to run 128core amber11 jobs on our very busy cluster
but his queue wait for 128 cores is going to be extremely long and he'd
probably get better perf on a single 64c (AMD Bulldozer) node that doesn't
have to communicate off-board.
We do have Mellanox&Voltaire QDR interconnects between 64c nodes, but still
the Q time and comm time are going to be significant. Any general real-life
observations that would push either approach?
Also, is there a suggested set of compilers and MPI versions that are
appropriate for amber11? gcc 4.4.7 (painfully) compiles the serial version,
but the openMPI version of the fortran compiler fails immediately on the
parallel version of sander:
root.hpc-s:/data/apps/amber/amber11/src
1457 $ make parallel
Starting installation of Amber11 (parallel) at Wed Sep 25 12:38:38 PDT 2013.
cd sander && make parallel
make[1]: Entering directory `/data/apps/amber/amber11/src/sander'
cpp -traditional constants.f > _constants.f
mpif90 -c -O3 -mtune=generic -o constants.o _constants.f
constants.f:24.1:
module constants
1
Error: Non-numeric character in statement label at (1)
constants.f:24.1:
module constants
1
Error: Unclassifiable statement at (1)
constants.f:28.1:
double precision, parameter :: TEN_TO_MINUS2 = 1.0d-2
1
Error: Non-numeric character in statement label at (1)
constants.f:28.1:
double precision, parameter :: TEN_TO_MINUS2 = 1.0d-2
1
Error: Unclassifiable statement at (1)
constants.f:29.1:
double precision, parameter :: TEN_TO_MINUS3 = 1.0d-3
1
[many such errors]
---
Harry Mangalam - Research Computing, OIT, Rm 225 MSTB, UC Irvine
[m/c 2225] / 92697 Google Voice Multiplexer: (949) 478-4487
415 South Circle View Dr, Irvine, CA, 92697 [shipping]
MSTB Lat/Long: (33.642025,-117.844414) (paste into Google Maps)
---
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Received on Wed Sep 25 2013 - 13:00:04 PDT
