[torqueusers] HELP setup on>>charmrun/mpirun & NAMD via torque

Dan Roberts Daniel.G.Roberts at sanofi-aventis.com
Mon Jul 30 09:38:42 MDT 2007


Hello All

When I try to compile charm++ using MPI I get the following errors
listed below..
What version of MPI are you using by the way?
Thanks
Dan


Below is what I attempted based on the NOTES included with the tar file
of charm/namd

Download TCL and FFTW libraries:
  mkdir fftw;  cd fftw
  wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux.tar.gz
  tar xzf fftw-linux.tar.gz
  cd ..;  mkdir tcl;  cd tcl
  wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl-linux.tar.gz
  tar xzf tcl-linux.tar.gz

Unpack NAMD and matching Charm++ source code and enter directory:
  tar xzf NAMD_2.6_Source.tar.gz
  cd NAMD_2.6_Source
  tar xf charm-5.9.tar
  cd charm-5.9

Build and test the Charm++/Converse library:
  ./build charm++ mpi-linux -no-shared-build DCMK_OPTIMIZE=1
  cd net-linux/pgms/charm++/megatest/
  make pgm
  cd ../../../../..

Edit various configuration files:
  vi Make.charm  (set CHARMBASE to .rootdir/charm-5.9 or full path to
charm)
  vi arch/Linux-i686.fftw     (fix library name and path to files)
  vi arch/Linux-i686.tcl      (fix library version and path to TCL
files)

Set up build directory and compile:
  ./config tcl fftw Linux-i686-MPI
  cd Linux-i686-MPI
  make


AND the above "make" command fails several times with this as the
conclusion:::



/usr/lib/gcc/i386-redhat-linux/3.4.5/../../../libc.a(malloc.o)(.text
+0x38a8): In  function `__malloc_check_init':
: multiple definition of `__malloc_check_init'
/global/bwsn001/home/users1/nm67371/NAMD_2.6_Source/charm-5.9/mpi-
linux/bin/../l ib/libmemory-default.o(.text+0x136b): first defined here
/usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed from
113 in /
global/bwsn001/home/users1/nm67371/NAMD_2.6_Source/charm-5.9/mpi-
linux/bin/../li b/libmemory-default.o to 154 in /usr/lib/gcc/i386-
redhat-linux/3.4.5/../../../li bc.a(malloc.o)
collect2: ld returned 1 exit status
Fatal Error by charmc in
directory /global/bw_1/home/users1/nm67371/NAMD_2.6_Sou rce/Linux-i686-
MPI
   Command mpiCC -rdynamic -L/global/bwsn002/software/ia32/tcl/linux/lib
-L/glob al/bw_1/home/users1/nm67371/tcl/lib -
L/global/bwsn002/software/ia32/fftw/linux/l ib -
L/global/bw_1/home/users1/nm67371/fftw/lib -
I/global/bwsn001/home/users1/nm6 7371/NAMD_2.6_Source/charm-5.9/mpi-
linux/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O 3 -march=pentiumpro -
ffast-math -static -o namd2 -L/global/bwsn001/home/users1/n
m67371/NAMD_2.6_Source/charm-5.9/mpi-linux/bin/../lib -
I/global/bwsn001/home/use rs1/nm67371/NAMD_2.6_Source/charm-5.9/mpi-
linux/bin/../include /global/bwsn001/h
ome/users1/nm67371/NAMD_2.6_Source/charm-5.9/mpi-
linux/bin/../lib/libldb-rand.o obj/buildinfo.o obj/common.o obj/dcdlib.o
obj/erf.o obj/fitrms.o obj/main.o obj/ mainfunc.o obj/memusage.o
obj/strlib.o obj/AlgSeven.o obj/AlgRecBisection.o obj/ AlgNbor.o
obj/AtomMap.o obj/BackEnd.o obj/BroadcastMgr.o obj/BroadcastClient.o o
bj/CollectionMaster.o obj/CollectionMgr.o obj/Communicate.o
obj/Compute.o obj/Co mputeAngles.o obj/ComputeBonds.o
obj/ComputeConsForce.o obj/ComputeConsForceMsgs .o
obj/ComputeCrossterms.o obj/ComputeCylindricalBC.o
obj/ComputeDihedrals.o obj /ComputeDPME.o obj/ComputeDPMEMsgs.o
obj/ComputeDPMTA.o obj/ComputeEField.o obj/ ComputeEwald.o
obj/ComputeExt.o obj/ComputeFullDirect.o obj/ComputeHomePatch.o o
bj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o
obj/ComputeGl obalMsgs.o obj/ComputeMap.o obj/ComputeMgr.o
obj/ComputeNonbondedSelf.o obj/Comp uteNonbondedPair.o
obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o obj/Comp
uteNonbondedFEP.o obj/ComputeNonbondedLES.o obj/ComputeNonbondedPProf.o
obj/Comp utePatch.o obj/ComputePatchPair.o obj/ComputePme.o
obj/ComputeRestraints.o obj/C omputeSphericalBC.o obj/ComputeStir.o
obj/ComputeTclBC.o obj/ConfigList.o obj/Co ntroller.o obj/ccsinterface.o
obj/DataStream.o obj/DumpBench.o obj/FreeEnergyAss ert.o
obj/FreeEnergyGroup.o obj/FreeEnergyLambda.o obj/FreeEnergyLambdMgr.o
obj/ FreeEnergyParse.o obj/FreeEnergyRestrain.o obj/FreeEnergyRMgr.o
obj/FreeEnergyVe ctor.o obj/GlobalMaster.o obj/GlobalMasterServer.o
obj/GlobalMasterTest.o obj/Gl obalMasterIMD.o obj/GlobalMasterTcl.o
obj/GlobalMasterSMD.o obj/GlobalMasterTMD. o
obj/GlobalMasterFreeEnergy.o obj/GlobalMasterEasy.o
obj/GlobalMasterMisc.o obj /GromacsTopFile.o obj/heap.o obj/HomePatch.o
obj/IMDOutput.o obj/InfoStream.o ob j/LdbCoordinator.o obj/LJTable.o
obj/Measure.o obj/MStream.o obj/MigrateAtomsMsg .o obj/Molecule.o
obj/NamdCentLB.o obj/NamdNborLB.o obj/NamdState.o obj/NamdOneT ools.o
obj/Node.o obj/Output.o obj/Parameters.o obj/ParseOptions.o obj/Patch.o
o bj/PatchMgr.o obj/PatchMap.o obj/PDB.o obj/PDBData.o obj/PmeBase.o
obj/PmeKSpace .o obj/PmeRealSpace.o obj/ProcessorPrivate.o
obj/ProxyMgr.o obj/ProxyPatch.o obj /Rebalancer.o obj/RecBisection.o
obj/ReductionMgr.o obj/RefineOnly.o obj/ScriptT cl.o obj/Sequencer.o
obj/Set.o obj/Settle.o obj/SimParameters.o obj/Sync.o obj/T clCommands.o
obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o
obj/dcdplugin.o moduleinit22281.o -lmoduleNeighborLB -
lmodulecommlib /global/bw
sn001/home/users1/nm67371/NAMD_2.6_Source/charm-5.9/mpi-
linux/bin/../lib/libmemo ry-
default.o /global/bwsn001/home/users1/nm67371/NAMD_2.6_Source/charm-5.9/mpi-l inux/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util  -lckqt -lmpich -ldl -ltcl8.3 -ldl -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmod ulecommlib -lm returned error code 1
charmc exiting...
rm -f moduleinit22281.C moduleinit22281.o
make: *** [namd2] Error 1
[nm67371 at bwdl01-m001 Linux-i686-MPI]$







On Fri, 2007-07-27 at 03:28 -0400, Chris Samuel wrote:
> On Thu, 26 Jul 2007, Daniel.G.Roberts at sanofi-aventis.com wrote:
> 
> > CHARMRUN=/global/bw_2/software/ia32/namd/NAMD_2.6b1_Linux-
> i686/charmrun
> 
> Do yourself a *big* favour - rebuild Charm++ to be an MPI version and
> then
> recompile NAMD against that.
> 
> Then you'll end up with NAMD being a native MPI program and you can
> use Pete
> Wyckoff's excellent mpiexec program to launch it.
> 
> That's our standard way of building NAMD here and it saves *so* much
> pain..
> 
> --
> Christopher Samuel - (03) 9925 4751 - Systems Manager
>  The Victorian Partnership for Advanced Computing
>  P.O. Box 201, Carlton South, VIC 3053, Australia
> VPAC is a not-for-profit Registered Research Agency
> 
> 
> plain text document attachment (ATT533175.txt), "ATT533175.txt"
> _______________________________________________
> torqueusers mailing list
> torqueusers at supercluster.org
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