AMBER Archive (2004)

Subject: Re: AMBER: pmemd and mpich - myrinet

From: Lubos Vrbka (shnek_at_tiscali.cz)
Date: Sat Apr 24 2004 - 05:50:02 CDT

bob,

> 1) There is no machinefile for xeons with myrinet simply because I did not
> have access to a xeons + myrinet installation. It is easy to make the
> appropriate modifications to Machine.mpich_gm_ifc (diff Machine.mpich_ifc
> and Machine.mpich_ifc_p4, and craft up your own Machine.mpich_gm_ifc_p4)
i tried to create my own Machine.mpich_gm_ifc_p4 according to your
instructions

...

setenv MPICH_HOME /software/mpich-1.2.5/build/LINUX/ch_gm_intel
setenv GM_HOME /packages/run/gm-1.6.3

...

setenv MPICH_INCLUDE $MPICH_HOME/include
setenv MPICH_LIBDIR $MPICH_HOME/lib
setenv MPICH_LIBDIR2 $GM_HOME/lib

setenv MACHINE LINUX_INTEL_P4
setenv MACH Linux
setenv MACHINEFLAGS "-DREGNML -DMPI -DNO_MPI_BUFFER_ALIASING
-DINTEL_P4_VECT_OPT"
setenv FFLAGS "-DSHORT=INTEGER(2) -DLOGICAL_BYTE=LOGICAL(1)"
setenv MACHINEFLAGS "$MACHINEFLAGS $FFLAGS"

# CPP is the cpp for this machine
setenv CPP "/lib/cpp -traditional -I$MPICH_INCLUDE"
setenv CC "gcc "
setenv LOADCC "gcc "

# SYSDIR is the name of the system-specific source directory relative to
src/*/
setenv SYSDIR Machines/intel

# COMPILER ALIASES:

# little or no optimization:
setenv L0 "ifc -c -auto -tpp7 -mp1 -O0"

# modest optimization (local scalar):
setenv L1 "ifc -c -auto -tpp7 -mp1 -O2"

# high scalar optimization (but not vectorization):
setenv L2 "ifc -c -auto -tpp7 -xW -mp1 -ip -O3"

# high optimization (may be vectorization, not parallelization):
setenv L3 "ifc -c -auto -tpp7 -xW -mp1 -ip -O3"

# LOADER/LINKER:
setenv LOAD "ifc -static"
setenv LOADLIB "-limf -lsvml -lPEPCF90 -L$MPICH_LIBDIR -lmpich
-L$MPICH_LIBDIR2 -lgm -lpthread"

# ranlib, if it exists
setenv RANLIB ranlib

pmemd builds fine. all 4 copies of the job (i'm running on 2 nodes of
dual xeon machines) are spawned correctly, but then:

All 4 tasks started.
read_gm_startup_ports: waiting for info
read_gm_startup_ports: mpich gm version 1248
read_gm_startup_ports: id 1 port 2 board 0 gm_node_id 19
   numanode 0 pid 12146 remote_port 0
read_gm_startup_ports: id 3 port 4 board 0 gm_node_id 19
   numanode 0 pid 12160 remote_port 0
[0] Error: Unable to open a GM port !
[0] Error: write to socket failed !
[2] Error: Unable to open a GM port !
[2] Error: write to socket failed !

and execution is aborted. it surprises me since the same version of gm
libraries works correctly on the same xeon machines with pmemd built
without xeon-specific options. i'm wondering whether there is some
problem with myrinet and i should ask the sysadmins of the cluster, or
the problem is somewhere in the machinefile...

regards, 

-- 
Lubos
_@_"
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