Charm++ parallel programming system

[Abhishek TYAGI <atyagiaa AT connect.ust.hk>]

Dear Jim,

Thankyou for the reply. For the updated version, do you have idea how the 
tutorial will work, I mean the tutorial is for mpirun. 

Thanks and regards
Abhi



________________________________________
From: Jim Phillips 
<jim AT ks.uiuc.edu>
Sent: Tuesday, December 22, 2015 12:17 AM
To: Abhishek TYAGI
Cc: 
charm AT cs.illinois.edu
Subject: Re: [ppl] [charm] Charm install Error

The REUS feature is now available with verbs-linux-x86_64 and
verbs-linux-x86_64-smp (for CUDA) Charm++ builds, so you should be able to
use the pre-built binaries that are available for download (the ones that
mention "multi-copy algorithms" in the comment).

Wait a few hours and you can get the 2.11 release.

Jim


On Mon, 21 Dec 2015, Abhishek TYAGI wrote:

> Dear Jim,
>
> For the NAMD-MPI compiling I am using NAMD-CSV source code. I want to 
> compile MPI version. The reason for compiling NAMD with MPI is to run "A 
> Tutorial on One-dimensional Replica-exchange Umbrella Sampling". According 
> to this tutorial mpirun will be implimented to execute REUS. Therefore, I 
> am compiling this version. The GPU cluster have the configuration to use 
> infiband. 
> (https://itsc.ust.hk/services/academic-teaching-support/high-performance-computing/gpu-cluster/hardware/)
>
> The command I had tried is as follows:
>
> [atyagiaa@login-0
>  charm-6.7.0]$ env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 
> --with-production
>
> [atyagiaa@login-0
>  charm-6.7.0]$ which mpicxx
> /usr/local/pgi/linux86-64/2013/mpi2/mpich/bin/mpicxx.
>
> The details of compilation of charm were attached herewith the mail.
>
> (For general molecular simulations, I am using NAMD 2.11b1 multicore-CUDA 
> build.)
>
> Thanks and regards
> Abhi
>
>
> ________________________________________
> From: Jim Phillips 
> <jim AT ks.uiuc.edu>
> Sent: Monday, December 21, 2015 10:02 PM
> To: Abhishek TYAGI
> Cc: 
> charm AT cs.illinois.edu
> Subject: Re: [ppl] [charm] Charm install Error
>
> Also, you should be using verbs-smp or net-ibverbs-smp on a GPU cluster.
>
> Jim
>
>
> On Mon, 21 Dec 2015, Phil Miller wrote:
>
>> 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
>>>
>>>
>>>
>>