Charm++ parallel programming system

[Phil Miller <mille121 AT illinois.edu>]

Hi Abhi,

Could you please provide the following extra information:
- what underlying compiler does your mpicxx call?

- what was the output of the configure script at the beginning of the build process?

With that, hopefully we can help resolve this.

Phil

On Mon, Dec 21, 2015 at 4:08 AM, Abhishek TYAGI <atyagiaa AT connect.ust.hk> wrote:

Hi,

I am trying to install charm-6.7.0 on GPU cluster here in our university. But I got the following error, I tried to change the input information, still the same error is coming, I am trying to compile NAMD for MPI on the cluster. For your information, mpirun and mpiexec were already installed on the cluster. As a user I have limited access. The error is as

../../../../bin/charmc -O -DCMK_OPTIMIZE=1  -o ../../../../lib/libmoduleCkMulticast.a ckmulticast.o
ar: creating ../../../../lib/libmoduleCkMulticast.a
/bin/cp CkMulticast.decl.h ../../../../include
/bin/cp CkMulticast.def.h ../../../../include
gmake[1]: Leaving directory `/d4/atyagiaa/NAMD_CVS-2015-12-17_Source/charm-6.7.0/mpi-linux-x86_64/tmp/libs/ck-libs/multicast'
/usr/bin/gmake -C libs/ck-libs/pythonCCS
gmake[1]: Entering directory `/d4/atyagiaa/NAMD_CVS-2015-12-17_Source/charm-6.7.0/mpi-linux-x86_64/tmp/libs/ck-libs/pythonCCS'
(CHARMINC=../../../../include;. $CHARMINC/conv-config.sh; \
    if test "$CMK_BUILD_PYTHON" != ""; then (/usr/bin/gmake conditional OPTS='-O -DCMK_OPTIMIZE=1 ' || exit 1); fi)
gmake[2]: Entering directory `/d4/atyagiaa/NAMD_CVS-2015-12-17_Source/charm-6.7.0/mpi-linux-x86_64/tmp/libs/ck-libs/pythonCCS'
gmake[2]: Nothing to be done for `conditional'.
gmake[2]: Leaving directory `/d4/atyagiaa/NAMD_CVS-2015-12-17_Source/charm-6.7.0/mpi-linux-x86_64/tmp/libs/ck-libs/pythonCCS'
gmake[1]: Leaving directory `/d4/atyagiaa/NAMD_CVS-2015-12-17_Source/charm-6.7.0/mpi-linux-x86_64/tmp/libs/ck-libs/pythonCCS'
/usr/bin/gmake -C libs/ck-libs/io
gmake[1]: Entering directory `/d4/atyagiaa/NAMD_CVS-2015-12-17_Source/charm-6.7.0/mpi-linux-x86_64/tmp/libs/ck-libs/io'
gmake[1]: Nothing to be done for `all'.
gmake[1]: Leaving directory `/d4/atyagiaa/NAMD_CVS-2015-12-17_Source/charm-6.7.0/mpi-linux-x86_64/tmp/libs/ck-libs/io'
/usr/bin/gmake -C libs/ck-libs/ckloop
gmake[1]: Entering directory `/d4/atyagiaa/NAMD_CVS-2015-12-17_Source/charm-6.7.0/mpi-linux-x86_64/tmp/libs/ck-libs/ckloop'
../../../../bin/charmc -O -DCMK_OPTIMIZE=1  -lpthread -I../../../../tmp -o CkLoop.o CkLoop.C
"CkLoop.h", line 105: error: identifier "__sync_add_and_fetch" is undefined
          return __sync_add_and_fetch(&curChunkIdx, 1);
                 ^

"CkLoop.h", line 119: error: identifier "__sync_add_and_fetch" is undefined
          __sync_add_and_fetch(&finishFlag, counter);
          ^

"CkLoop.h", line 264: warning: statement is unreachable
          return NULL;
          ^

"CkLoop.C", line 18: error: identifier "__thread" is undefined
  static __thread pthread_cond_t thdCondition; //the signal var of each pthread to be notified
         ^

"CkLoop.C", line 18: error: "pthread_cond_t" has already been declared in the
          current scope
  static __thread pthread_cond_t thdCondition; //the signal var of each pthread to be notified
                  ^

"CkLoop.C", line 18: error: expected a ";"
  static __thread pthread_cond_t thdCondition; //the signal var of each pthread to be notified
                                 ^

"CkLoop.C", line 19: error: identifier "__thread" is undefined
  static __thread pthread_mutex_t thdLock; //the lock associated with the condition variables
         ^

"CkLoop.C", line 19: error: "pthread_mutex_t" has already been declared in the
          current scope
  static __thread pthread_mutex_t thdLock; //the lock associated with the condition variables
                  ^

"CkLoop.C", line 19: error: expected a ";"
  static __thread pthread_mutex_t thdLock; //the lock associated with the condition variables
                                  ^

"CkLoop.C", line 27: error: variable "pthread_mutex_t" is not a type name
  static pthread_mutex_t **allLocks = NULL;
         ^

"CkLoop.C", line 28: error: variable "pthread_cond_t" is not a type name
  static pthread_cond_t **allConds = NULL;
         ^

"CkLoop.C", line 64: error: identifier "thdLock" is undefined
      pthread_mutex_init(&thdLock, NULL);
                          ^

"CkLoop.C", line 65: error: identifier "thdCondition" is undefined
      pthread_cond_init(&thdCondition, NULL);
                         ^

"CkLoop.C", line 70: error: identifier "__sync_add_and_fetch" is undefined
      __sync_add_and_fetch(&gCrtCnt, 1);
      ^

"CkLoop.C", line 93: warning: missing return statement at end of non-void
          function "ndhThreadWork"
  }
  ^

"CkLoop.C", line 98: error: expected an _expression_
      allLocks = (pthread_mutex_t **)malloc(sizeof(void *)*numThreads);
                                    ^

"CkLoop.C", line 98: error: expected a ";"
      allLocks = (pthread_mutex_t **)malloc(sizeof(void *)*numThreads);
                                     ^

"CkLoop.C", line 99: error: expected an _expression_
      allConds = (pthread_cond_t **)malloc(sizeof(void *)*numThreads);
                                   ^

"CkLoop.C", line 99: error: expected a ";"
      allConds = (pthread_cond_t **)malloc(sizeof(void *)*numThreads);
                                    ^

"CkLoop.def.h", line 88: warning: variable "newmsg" was declared but never
          referenced
  CharmNotifyMsg *newmsg = (CharmNotifyMsg *)this;
                  ^

"CkLoop.def.h", line 123: warning: variable "newmsg" was declared but never
          referenced
  HelperNotifyMsg *newmsg = (HelperNotifyMsg *)this;
                   ^

"CkLoop.def.h", line 158: warning: variable "newmsg" was declared but never
          referenced
  DestroyNotifyMsg *newmsg = (DestroyNotifyMsg *)this;
                    ^

"CkLoop.C", line 38: warning: function "HelperOnCore" was declared but never
          referenced
  static int HelperOnCore() {
             ^

17 errors detected in the compilation of "CkLoop.C".
Fatal Error by charmc in directory /d4/atyagiaa/NAMD_CVS-2015-12-17_Source/charm-6.7.0/mpi-linux-x86_64/tmp/libs/ck-libs/ckloop
   Command mpicxx -DCMK_GFORTRAN -I../../../../bin/../include -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -I../../../../tmp -O -c CkLoop.C -o CkLoop.o returned error code 2
charmc exiting...
gmake[1]: *** [CkLoop.o] Error 1
gmake[1]: Leaving directory `/d4/atyagiaa/NAMD_CVS-2015-12-17_Source/charm-6.7.0/mpi-linux-x86_64/tmp/libs/ck-libs/ckloop'
gmake: *** [ckloop] Error 2

Please suggest me what to do?

Thanks in advance

Abhi

Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong