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Re: [charm] [ppl] Charm install Error


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  • From: Abhishek TYAGI <atyagiaa AT connect.ust.hk>
  • To: Jim Phillips <jim AT ks.uiuc.edu>
  • Cc: "charm AT cs.illinois.edu" <charm AT cs.illinois.edu>
  • Subject: Re: [charm] [ppl] Charm install Error
  • Date: Sat, 23 Jan 2016 19:03:56 +0000
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Dear Jim,

I am running this version sucessfully on GPU Cluster, however I am not able
to execute binaries with Linux-x86_64-netlrts (Multi-copy algorithms). This
can only run on CPU version. I am not able to add GPU in this. Can you
suggest how to make it work.
The gpu cluster : 4 GPU K20 and 2 E series CPU 32 cores.

Abhishek Tyagi
PhD Student
Chemical and Biomolecular Engineering
Hong Kong University of Science and Technology
Clear Water Bay, Hong Kong


________________________________________
From: Jim Phillips
<jim AT ks.uiuc.edu>
Sent: Tuesday, December 22, 2015 12:19 PM
To: Abhishek TYAGI
Cc:
charm AT cs.illinois.edu
Subject: Re: [ppl] [charm] Charm install Error

You would run NAMD using charmrun. Directions are in the release notes.

Jim

On Tue, 22 Dec 2015, Abhishek TYAGI wrote:

> 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 AT login-0
>> charm-6.7.0]$ env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64
>> --with-production
>>
>> [atyagiaa AT 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
>>>>
>>>>
>>>>
>>>
>


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