Charm++ parallel programming system

[Bo Zhang <zhang416 AT indiana.edu>]

Hello Jim,

I swap and load the modules as you suggested. And I rebuilt the package several times: 

Thu Aug 29 14:18:14 EDT 2013

Using the following build command:

./build charm++ gemini_gni-crayxe craycc   hugepages   -j16  --with-production

Thu Aug 29 14:48:27 EDT 2013

Using the following build command:

./build charm++ gemini_gni-crayxe craycc  smp   persistent hugepages   -j16  --with-production

Thu Aug 29 14:59:20 EDT 2013

Using the following build command:

./build charm++ gemini_gni-crayxe   smp   persistent hugepages   -j16  --with-production

Each time, the built was successful. But I still cannot make the simplesayhello example. For the last set of build options I used, I got the following the messages: 

zhang416@login1:~/repository/charm/gemini_gni-crayxe-hugepages-persistent-smp/tests/charm++/simplearrayhello> make

../../../bin/charmc   hello.ci

../../../bin/charmc  -c hello.C

../../../bin/charmc  -language charm++ -o hello hello.o

../../../bin/../lib/libconv-util.a(sockRoutines.o): In function `skt_lookup_ip':

sockRoutines.c:(.text+0x3a3): warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking

../../../bin/../lib/libconv-util.a(persist-comm.o): In function `compressFloatingPoint':

persist-comm.c:(.text+0x2f3): undefined reference to `assert'

../../../bin/../lib/libconv-util.a(persist-comm.o): In function `compressDouble':

persist-comm.c:(.text+0x451): undefined reference to `assert'

collect2: error: ld returned 1 exit status

Fatal Error by charmc in directory /N/u/zhang416/BigRed2/repository/charm/gemini_gni-crayxe-hugepages-persistent-smp/tests/charm++/simplearrayhello

   Command CC -I/opt/cray/rca/1.0.0-2.0401.38656.2.2.gem/include -I/opt/cray/pmi/4.0.1-1.0000.9421.73.3.gem/include -I/opt/cray-hss-devel/7.0.0/include -I/opt/cray/krca/1.0.0-2.0401.36792.3.70.gem/include -I/opt/cray/gni-headers/2.1-1.0401.5675.4.4.gem/include -I/opt/cray/ugni/4.0-1.0401.5928.9.5.gem/include -D_REENTRANT -rdynamic -o hello -L../../../bin/../lib -I../../../bin/../include ../../../bin/../lib/libldb-rand.o hello.o moduleinit22274.o ../../../bin/../lib/libmemory-default.o ../../../bin/../lib/libthreads-default.o -lckmain -lck -lconv-cplus-y -lconv-core -lconv-util ../../../bin/../lib/custom_partitioner.o -lckqt -lpthread -lrt -lz -ldl -lm returned error code 1

charmc exiting...

make: *** [hello] Error 1

I look forward to hearing further instructions from you. Thank you. 

Bo 

On Aug 29, 2013, at 2:30 PM, Jim Phillips wrote:

For NAMD we use these modules:

module swap PrgEnv-cray PrgEnv-gnu
module load rca
module load craype-hugepages8M

And these sets of options:

gemini_gni-crayxe hugepages persistent

gemini_gni-crayxe hugepages persistent smp

-Jim


On Thu, 29 Aug 2013, Phil Miller wrote:

Going on what I can remember and intuit from what I see here, you may

need to add the build option 'hugepages' to your build command. You

should also ensure that you have one of the craype-hugepages* modules

loaded.

I'm not sure why this error appeared though, and will check with the

rest of the team on how we can prevent it in the future.

Thanks, and I hope that helps

Phil

On Thu, Aug 29, 2013 at 12:59 PM, Bo Zhang <zhang416 AT indiana.edu> wrote:

Dear developing team:

This is Bo Zhang from Indiana University. I am trying to install charm++

locally on a Cray XE6/XK7 machine. The build command used is:

'./build charm++ gemini_gni-crayxe craycc      -j16  --with-production'

After running the command, it shows that charm++ was built successfully.

Next, I followed the suggestion to try the sample program

'gemini_gni-crayxe-craycc/tests/charm++/simplearrayhello', but the make was

terminated with error.

zhang416@login1:~/repository/charm/tests/charm++/simplearrayhello> make

../../../bin/charmc   hello.ci

../../../bin/charmc  -c hello.C

../../../bin/charmc  -language charm++ -o hello hello.o

/opt/cray/xe-sysroot/4.1.40/usr/lib64/libhugetlbfs.a(hugeutils.o): In

function `gethugepagesize':

/usr/src/packages/BUILD/cray-libhugetlbfs-2.11/hugeutils.c:863: multiple

definition of `gethugepagesize'

../../../bin/../lib/cray_tlbhack.o:(.text+0x0): first defined here

/opt/cray/xe-sysroot/4.1.40/usr/lib64/libpthread.a(sem_open.o): In function

`sem_open':

/usr/src/packages/BUILD/glibc-2.11.3/nptl/sem_open.c:333: warning: the use

of `mktemp' is dangerous, better use `mkstemp'

../../../bin/../lib/libconv-util.a(sockRoutines.o): In function

`skt_lookup_ip':

/N/hd00/zhang416/BigRed2/repository/charm/gemini_gni-crayxe-craycc/tmp/sockRoutines.c:295:

warning: Using 'gethostbyname' in statically linked applications requires at

runtime the shared libraries from the glibc version used for linking

Fatal Error by charmc in directory

/N/u/zhang416/BigRed2/repository/charm/tests/charm++/simplearrayhello

  Command CC -I/opt/cray/rca/1.0.0-2.0401.38656.2.2.gem/include

-I/opt/cray/pmi/4.0.1-1.0000.9421.73.3.gem/include

-I/opt/cray-hss-devel/7.0.0/include

-I/opt/cray/krca/1.0.0-2.0401.36792.3.70.gem/include

-I/opt/cray/gni-headers/2.1-1.0401.5675.4.4.gem/include

-I/opt/cray/ugni/4.0-1.0401.5928.9.5.gem/include -o hello

-L../../../bin/../lib -I../../../bin/../include

../../../bin/../lib/libldb-rand.o hello.o moduleinit44124.o

../../../bin/../lib/libmemory-default.o

../../../bin/../lib/libthreads-default.o -lckmain -lck -lconv-cplus-y

-lconv-core -lconv-util ../../../bin/../lib/custom_partitioner.o -lckqt -ldl

-lrt ../../../bin/../lib/cray_tlbhack.o -lm returned error code 1

charmc exiting...

make: *** [hello] Error 1

Would you please let me know how to resolve this issue? Thank you very much.

Sincerely,

Bo

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