Charm++ parallel programming system

[Dow Hurst DPHURST <DPHURST AT uncg.edu>]

I meant to show my PATH as containing:

/usr/mpi/gcc/mvapich-0.9.9/bin

so that mpiCC is found.  Sorry about truncating that bit of data!
Dow

__________________________________


-----charm-bounces AT cs.uiuc.edu
 wrote: -----

To: 
charm AT cs.uiuc.edu
From: Dow Hurst DPHURST 
<DPHURST AT uncg.edu>
Sent by: 
charm-bounces AT cs.uiuc.edu
Date: 08/31/2007 02:47AM
Subject: [charm] charmm++ 5.9 compile failure


I'm having a bit of trouble with building charm++ using mvapich-0.9.9
compiled with gcc.  I only have the mvapich-0.9.9 in my path and no other
implementation of MPI.

The cluster is Mellanox's test cluster with AMD dual core opterons
outfitted with the Infiniband Connectix cards.  My PATH is:

PATH=/usr/lib64/qt-3.3
/bin:/usr/kerberos/bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/mpi/gcc/mvapich-0.9.9



Here is my failed build containing error messages I've never seen before.
Thanks for your help!

./build charm++ mpi-linux-amd64 -O -nobs
Creating dir: mpi-linux-amd64
Creating dir: mpi-linux-amd64/tmp
Copying src/scripts/Makefile to mpi-linux-amd64/tmp
Soft-linking over bin
Soft-linking over lib
Soft-linking over lib_so
Soft-linking over include
Soft-linking over tmp
Generating mpi-linux-amd64/tmp/conv-mach-pre.sh
Generating mpi-linux-amd64/tmp/conv-mach-opt.h, conv-mach-opt.sh
Performing 'make  charm++ OPTS= -O -nobs' in mpi-linux-amd64/tmp
rm -f .gdir
(cd .. ; basename "`pwd`" | sed -e 
's@-.*@@')
   > .gdir
pwd
/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp
find . -type l -exec rm {} \;
rm -rf QuickThreads
rm -rf libs
rm -rf ../bin ; mkdir ../bin
rm -rf ../lib ; mkdir ../lib
rm -rf ../lib_so ; mkdir ../lib_so; touch ../lib_so/.charmso
rm -rf ../examples
rm -rf ../tests
rm -rf ../doc ; ln -s ../doc ../doc
../../src/scripts/gatherflat ../../src/scripts .
./gatherflat ../../src/conv-core        .
./gatherflat ../../src/conv-ldb         .
./gatherflat ../../src/conv-ccs         .
./gatherflat ../../src/conv-perf        .
./gatherflat ../../src/ck-core          .
./gatherflat ../../src/util             .
./gatherflat ../../src/ck-perf          .
./gatherflat ../../src/ck-ldb           .
./gatherflat ../../src/ck-com           .
./gatherflat ../../src/conv-com           .
./gatherflat ../../src/langs/simplemsg  .
./gatherflat ../../src/langs/pvmc       .
./gatherflat ../../src/langs/bluegene   .
./gatherflat ../../src/langs/f90charm   .
./gatherflat ../../src/xlat-i           .
./gatherflat ../../src/xlatcpm          .
./gathertree ../../src/QuickThreads QuickThreads
./gathertree ../../src/libs libs
./gathertree ../../src/arch/util      .
./gathertree ../../src/langs langs
./gathertree ../../src/langs/jade langs/jade
./gathertree ../../src/arch/common           .
./gathertree ../../src/arch/`cat .gdir`      .
./gatherflat ../../src/arch/`cat .vdir`      .
./gathertree ../../examples ../examples
./gathertree ../../tests ../tests
rm -f ../bin/dep.pl ; cp dep.pl ../bin/
chmod +x charmc
./system_ln  ../tmp/charmc ../bin/
ln -s ../../java/bin charmjavabin
ln -s ../../java/bin ../bin/charmjavabin
ln -s charmjavabin/* ../bin/
ln -s ../java ..
rm -f .gdir
rm -rf ../include ; mkdir ../include
./system_ln  ../tmp/conv-*.*h ../include
./system_ln  ../tmp/cc-*.*h ../include
if [ ! -f conv-common.h ] ; then ( touch conv-common.h ) ; fi
touch dirs+sources
make headerlinks
make[1]: Entering directory
`/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp'
make[1]: Warning: File `dirs+sources' has modification time 2.6e+04 s in
the future
./configure
checking machine name... mpi-linux-amd64
set C++ compiler as: mpiCC -m64 -fPIC
checking "whether C++ compiler works"... "ok"
set C++ linker as: mpiCC -m64 -fPIC
checking "whether linker works"... "ok"
checking "whether C++ bool works"... "ok"
checking "whether long long works"... "ok"
checking "whether __int64 works"... "no"
checking "whether long double works"... "ok"
checking "whether C++ class explicit keyword works"... "ok"
checking "whether C++ signed char and char differ"... "yes"
checking "whether C++ *_casts<> work"... "ok"
checking "whether templated member functions work"... "no"
checking "whether including STL <foo> works"... "ok"
checking "whether the std:: names for STL work"... "ok"
checking "whether namespaces work"... "ok"
checking "whether typeinfo/typeid works"... "ok"
checking "whether operator delete can be overloaded in same class"... "ok"
checking "whether GCC x86 assembly works"... "yes"
checking "whether GCC IA64 assembly works"... "no"
checking "whether it has mkstemp"... "yes"
checking "whether the poll() syscall exists"... "yes"
checking "whether the setpriority() exists"... "yes"
checking "whether to use signal-safe system() "... "yes"
checking "whether dlopen links without -ldl"... "yes"
checking "whether dlopen links with -ldl"... "yes"
checking "whether getProcAddress works"... "no"
checking "whether it has socklen_t"... "yes"
checking "whether the mmap() syscall exists"... "yes"
checking "whether mmap() accepts MAP_ANON"... "yes"
checking "whether glibc backtrace works"... "yes"
checking "whether it has zlib"... "yes"
checking "whether has values.h "... "yes"
checking "whether has alloca.h "... "yes"
checking "whether has malloc.h "... "yes"
checking "whether has elf.h "... "yes"
checking "whether has stdint.h "... "yes"
checking "whether Python is installed"... "no"
checking "whether it can build shared library"... "yes"
checking for sync... sync
checking subroutine name used by Fortran compiler... "Fortran compiler not
working"
configure: creating ./config.status
config.status: creating conv-autoconfig.h
../bin/charmc -host  xi-main.C
../bin/charmc -host  xi-symbol.C
../bin/charmc -host  xi-grammar.tab.C
../bin/charmc -host  -I. -DYY_NEVER_INTERACTIVE xi-scan.C
../bin/charmc -host  xi-util.C
../bin/charmc -host  -c sdag-globals.C
../bin/charmc -host  -c CSdagConstruct.C
../bin/charmc -host  -c CEntry.C
../bin/charmc -host  -language c++ -cp ../bin/ -o charmxi xi-main.o
xi-symbol.o xi-grammar.tab.o xi-scan.o xi-util.o sdag-globals.o
CSdagConstruct.o CEntry.o
../bin/charmc -intrinsic -O -nobs  ckcallback.ci
../bin/charmc -intrinsic -O -nobs  ckmarshall.ci
../bin/charmc -intrinsic -O -nobs  ckarray.ci
../bin/charmc -intrinsic -O -nobs  cklocation.ci
../bin/charmc -intrinsic -O -nobs  ckreduction.ci
../bin/charmc -intrinsic -O -nobs  ckarrayreductionmgr.ci
../bin/charmc -intrinsic -O -nobs  tempo.ci
../bin/charmc -intrinsic -O -nobs  waitqd.ci
../bin/charmc -intrinsic -O -nobs  ckfutures.ci
../bin/charmc -intrinsic -O -nobs  ckcheckpoint.ci
../bin/charmc -intrinsic -O -nobs  ckmemcheckpoint.ci
../bin/charmc -intrinsic -O -nobs  LBDatabase.ci
../bin/charmc -intrinsic -O -nobs  CentralLB.ci
../bin/charmc -intrinsic -O -nobs  ComboCentLB.ci
../bin/charmc -intrinsic -O -nobs  NullLB.ci
../bin/charmc -intrinsic -O -nobs  RandCentLB.ci
../bin/charmc -intrinsic -O -nobs  RecBisectBfLB.ci
../bin/charmc -intrinsic -O -nobs  BaseLB.ci
../bin/charmc -intrinsic -O -nobs  MetisLB.ci
../bin/charmc -intrinsic -O -nobs  DummyLB.ci
../bin/charmc -intrinsic -O -nobs  RotateLB.ci
../bin/charmc -intrinsic -O -nobs  RefineLB.ci
../bin/charmc -intrinsic -O -nobs  RefineKLB.ci
../bin/charmc -intrinsic -O -nobs  RefineCommLB.ci
../bin/charmc -intrinsic -O -nobs  OrbLB.ci
../bin/charmc -intrinsic -O -nobs  GreedyLB.ci
../bin/charmc -intrinsic -O -nobs  GreedyCommLB.ci
../bin/charmc -intrinsic -O -nobs  Comm1LB.ci
../bin/charmc -intrinsic -O -nobs  GreedyAgentLB.ci
../bin/charmc -intrinsic -O -nobs  GridCommLB.ci
../bin/charmc -intrinsic -O -nobs  PhasebyArrayLB.ci
../bin/charmc -intrinsic -O -nobs  TopoLB.ci
../bin/charmc -intrinsic -O -nobs  RefineTopoLB.ci
../bin/charmc -intrinsic -O -nobs  TopoCentLB.ci
../bin/charmc -intrinsic -O -nobs  NborBaseLB.ci
../bin/charmc -intrinsic -O -nobs  NeighborLB.ci
../bin/charmc -intrinsic -O -nobs  NeighborCommLB.ci
../bin/charmc -intrinsic -O -nobs  HybridBaseLB.ci
../bin/charmc -intrinsic -O -nobs  HybridLB.ci
../bin/charmc -intrinsic -O -nobs  WSLB.ci
../bin/charmc -intrinsic -O -nobs  EveryLB.ci
../bin/charmc -intrinsic -O -nobs  charisma.ci
../bin/charmc -intrinsic -O -nobs  trace-summary.ci
../bin/charmc -intrinsic -O -nobs  BlueGene.ci
../bin/charmc -intrinsic -O -nobs  ComlibManager.ci
Soft-linking headers...
touch headerlinks
make[1]: warning:  Clock skew detected.  Your build may be incomplete.
make[1]: Leaving directory
`/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp'
touch basics
make charm-target
make[1]: Entering directory
`/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp'
make[1]: Warning: File `basics' has modification time 2.6e+04 s in the
future
make headerlinks
make[2]: Entering directory
`/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp'
make[2]: Warning: File `headerlinks' has modification time 2.6e+04 s in the
future
make[2]: `headerlinks' is up to date.
make[2]: warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory
`/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp'
touch basics
make QuickThreads/libqt.a
make[2]: Entering directory
`/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp'
make[2]: Warning: File `conv-autoconfig.h' has modification time 2.6e+04 s
in the future
cd QuickThreads;./configure
rm -f QuickThreads/libqt.a
cd QuickThreads ; make qt  OPTS='-O -nobs '
make[3]: Entering directory
`/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp/QuickThreads'
make[3]: Warning: File `Makefile' has modification time 2.6e+04 s in the
future
rm -f qtmd.h
../system_ln  md/setjmp_d.h qtmd.h
../../bin/charmc -seq -I. -O -nobs  -c -o qt.o qt.c
../../bin/charmc -seq -I. -O -nobs  -c -o qtmds.o md/setjmp64.c
md/setjmp64.c: In function ‘qt_args_1’:
md/setjmp64.c:52: warning: incompatible implicit declaration of built-in
function ‘alloca’
md/setjmp64.c:53: warning: passing argument 1 of ‘longjmp’ from
incompatible pointer type
md/setjmp64.c: In function ‘qt_args’:
md/setjmp64.c:68: warning: incompatible implicit declaration of built-in
function ‘alloca’
md/setjmp64.c: In function ‘qt_block’:
md/setjmp64.c:87: warning: incompatible implicit declaration of built-in
function ‘alloca’
md/setjmp64.c:88: warning: passing argument 1 of ‘longjmp’ from
incompatible pointer type
md/setjmp64.c: In function ‘qt_abort’:
md/setjmp64.c:100: warning: incompatible implicit declaration of built-in
function ‘alloca’
md/setjmp64.c:101: warning: passing argument 1 of ‘longjmp’ from
incompatible pointer type
CHARMINC=..; . ../conv-config.sh;       \
        ../../bin/charmc -seq -I. -shared -O -nobs  -o
libqt.$CMK_SHARED_SUF qt.o qtmds.o
../../bin/charmc -seq -I. -O -nobs  -o libqt.a qt.o qtmds.o
ar: creating libqt.a
make[3]: warning:  Clock skew detected.  Your build may be incomplete.
make[3]: Leaving directory
`/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp/QuickThreads'
cp QuickThreads/libqt.a ../lib/libckqt.a
(CHARMINC=.; . ./conv-config.sh; \
          test -d ../lib_so && \
          cp QuickThreads/libqt.$CMK_SHARED_SUF ../lib_so && \
          cp QuickThreads/libqt.$CMK_SHARED_SUF
          ../lib_so/libckqt.$CMK_SHARED_SUF)
cp: cannot stat `QuickThreads/libqt.so': No such file or directory
make[2]: [QuickThreads/libqt.a] Error 1 (ignored)
make[2]: warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory
`/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp'
make converse-target
make[2]: Entering directory
`/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp'
make[2]: Warning: File `conv-autoconfig.h' has modification time 2.6e+04 s
in the future
../bin/charmc  -O -nobs  -c -I. convcore.c
../bin/charmc  -O -nobs  -c -I. conv-conds.c
../bin/charmc  -O -nobs  -c -I. queueing.c
../bin/charmc  -O -nobs  -c -I. msgmgr.c
../bin/charmc  -O -nobs  -c -I. cpm.c
../bin/charmc  -O -nobs  -c -I. cpthreads.c
cpthreads.c: In function ‘Cpthread_start_main’:
cpthreads.c:608: warning: cast to pointer from integer of different size
../bin/charmc  -O -nobs  -c -I. futures.c
../bin/charmc  -O -nobs  -c -I. cldb.c
../bin/charmc  -O -nobs  -c -I. topology.C
../bin/charmc  -O -nobs  -c -I. random.c
../bin/charmc  -O -nobs  -c -I. debug-conv.c
../bin/charmc  -O -nobs  -c -I. generate.c
../bin/charmc  -O -nobs  -c -I. edgelist.c
../bin/charmc  -O -nobs  -c -I. conv-ccs.c
../bin/charmc  -O -nobs  -c -I. ccs-builtins.C
../bin/charmc  -O -nobs  -c -I. traceCore.C
traceCore.h:20: error: previous declaration of ‘int Cpv__traceCoreOn_ [2]’
with ‘C++’ linkage
traceCoreAPI.h:8: error: conflicts with new declaration with ‘C’ linkage
Fatal Error by charmc in directory
/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp
   Command mpiCC -m64 -fPIC -I../bin/../include -D__CHARMC__=1 -I. -O -c
traceCore.C -o traceCore.o returned error code 1
charmc exiting...
make[2]: *** [traceCore.o] Error 1
make[2]: Leaving directory
`/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp'
make[1]: *** [converse] Error 2
make[1]: Leaving directory
`/home/demo/dhurst/build-namd01/NAMD_2.6_Source/charm-5.9
/mpi-linux-amd64/tmp'
make: *** [charm++] Error 2
-------------------------------------------------
Charm++ NOT BUILT. Either cd into mpi-linux-amd64/tmp and try
to resolve the problems yourself, visit
    http://charm.cs.uiuc.edu/
for more information. Otherwise, email the developers at 
ppl AT cs.uiuc.edu

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