Charm++ parallel programming system

[Bo Zhang <zhang416 AT indiana.edu>]

Phil,

I downloaded the 6.5.1 released version and built it with 

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

And I got the following error this time. 

zhang416@login1:~/charm-6.5.1/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

zhang416@login1:~/charm-6.5.1/gemini_gni-crayxe-hugepages-persistent-smp/tests/charm++/simplearrayhello> ./hello

libhugetlbfs [login1:38222]: WARNING: No mount point found for default huge page size. Using first available mount point.

libhugetlbfs [login1:38222]: WARNING: Hugepage size 2097152 unavailablelibhugetlbfs [login1:38222]: WARNING: Hugepage size 2097152 unavailableSegmentation fault

I am sorry to bother you this much. I thank you very much for helping me with this. 

Bo 

P.S. :

Currently Loaded Modulefiles:

  1) modules/3.2.6.7                         18) csa/3.0.0-1_2.0401.37452.4.50.gem

  2) eswrap/1.0.20-1.010101.433.0            19) job/1.5.5-0.1_2.0401.35380.1.10.gem

  3) craype-network-gemini                   20) xpmem/0.1-2.0401.36790.4.3.gem

  4) PrgEnv-gnu/4.1.40                       21) gni-headers/2.1-1.0401.5675.4.4.gem

  5) atp/1.6.3                               22) dmapp/3.2.1-1.0401.5983.4.5.gem

  6) xe-sysroot/4.1.40                       23) pmi/4.0.1-1.0000.9421.73.3.gem

  7) switch/1.0-1.0401.36779.2.72.gem        24) ugni/4.0-1.0401.5928.9.5.gem

  8) shared-root/1.0-1.0401.37253.3.50.gem   25) udreg/2.3.2-1.0401.5929.3.3.gem

  9) pdsh/2.26-1.0401.37449.1.1.gem          26) xt-libsci/12.1.01

 10) nodehealth/5.0-1.0401.38460.12.18.gem   27) gcc/4.8.1

 11) lbcd/2.1-1.0401.35360.1.2.gem           28) xt-asyncpe/5.22

 12) hosts/1.0-1.0401.35364.1.115.gem        29) craype-interlagos

 13) configuration/1.0-1.0401.35391.1.2.gem  30) cray-mpich/6.0.1

 14) ccm/2.2.0-1.0401.37254.2.142            31) moab/7.2.3

 15) audit/1.0.0-1.0401.37969.2.32.gem       32) torque/4.2.3.1

 16) rca/1.0.0-2.0401.38656.2.2.gem          33) craype-hugepages8M

 17) dvs/1.8.6_0.9.0-1.0401.1401.1.120

On Aug 29, 2013, at 3:25 PM, Phil Miller wrote:

I just pushed the fix for the 'undefined reference to assert' error.
If you wish to continue using the development version, please pull and
rebuild.

As Jim mentioned, it may be easier to simply use the released version
of Charm++ instead.

On Thu, Aug 29, 2013 at 2:09 PM, Phil Miller <mille121 AT illinois.edu> wrote:

The undefined references to 'assert' are the result of a recent

change, that will be fixed quickly.

On Thu, Aug 29, 2013 at 2:07 PM, Bo Zhang <zhang416 AT indiana.edu> wrote:

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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