I am replying to myself.
I have installed AMBER bugfixes. Reconfigured pmemd.cuda and added the aforementioned
lib flags in the config.h file. This time pmemd.cuda installed well and passed the tests..
Regards,
Cenk Andac, M.S., Ph.D.
Asst. Professor of Medical Pharmacology
Department of Medical Pharmacology
School of Medicine, Mevlana University, Konya
Turkiye 42003
Cell: +90-(536)-4813012
E-Mail:cenk_andac.yahoo.com
Web : http://med.mevlana.edu.tr/personel.asp?ID=1
________________________________
From: Cenk (Jenk) Andac <cenk_andac.yahoo.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, May 16, 2013 9:11 AM
Subject: Re: [AMBER] pmemd.CUDA installation problem
Hi Jason,
I added the libraries you suggested in the config.h file.
Then pmemd.cuda was installed OK. Thank you!
However the pmemd.cuda does not pass the tests.
Here is the error message I get after typing 'make test.cuda'
Using default PREC_MODEL = SPDP
make[2]: Entering directory `/usr/local/amber12/test'
cd cuda && make -k test.pmemd.cuda PREC_MODEL=SPDP
make[3]: Entering directory `/usr/local/amber12/test/cuda'
------------------------------------
Running CUDA Implicit solvent tests.
Precision Model = SPDP
------------------------------------
cd gb_ala3/ && ./Run.igb1_ntc1_min SPDP /usr/local/amber12/include/netcdf.mod
Currently only GPU SM Revisions 1.3 and 2.X are supported.
./Run.igb1_ntc1_min: Program error
make[3]: *** [test.pmemd.cuda.gb.serial] Error 1
My Graphics Card is NVIDIAGTX680 which I think supports
GPU SM Revision 3.0.
Any idea how I can cope with this?
Regards,
Cenk Andac, M.S., Ph.D.
Asst. Professor of Medical Pharmacology
Department of Medical Pharmacology
School of Medicine, Mevlana University, Konya
Turkiye 42003
Cell: +90-(536)-4813012
E-Mail:cenk_andac.yahoo.com
Web : http://med.mevlana.edu.tr/personel.asp?ID=1
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: Cenk (Jenk) Andac <cenk_andac.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, May 15, 2013 8:03 PM
Subject: Re: [AMBER] pmemd.CUDA installation problem
Try adding the following to the end of the PMEMD_CU_LIBS variable in your
config.h file:
-L/usr/lib64 -lstdc++
Then try re-compiling.
The problem is that the standard C++ functions could not be found by the
linker...
HTH,
Jason
On Wed, May 15, 2013 at 12:38 PM, Cenk (Jenk) Andac <cenk_andac.yahoo.com>wrote:
> Dear all,
>
> I have recently purchased an NVIDIA GTX680 Graphiics card and installed it
> on my desktop
> OS is OpenSuse 12.1. I have installed the NVIDIA ToolsKit 5 as well as the
> driver for the new graphics card.
> I set the environment to point to /usr/local/cuda for CUDA_HOME,
> $CUDA_HOME/bin for the binaries and $CUDA_HOME/lib & lib64 for CUDA
> libraries
>
> I use Intel fortran and cc compilers v13
>
> Basically AMBER12 serial and parallel installations went OK and passed the
> tests..
>
>
> I configured AMBER12 CUDA as follows
>
> ./configure -cuda intel
>
> everything seems to be OK in the config.h file.
>
> NVCC=$(CUDA_HOME)/bin/nvcc -use_fast_math -O3 -gencode
> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20
> PMEMD_CU_INCLUDES=-I$(CUDA_HOME)/include -IB40C -IB40C/KernelCommon
> PMEMD_CU_LIBS=-L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft
> -lcudart ./cuda/cuda.a
> PMEMD_CU_DEFINES=-DCUDA
>
> #PMEMD Specific build flags
> PMEMD_F90=ifort -DMKL -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
> -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT
> PMEMD_FOPTFLAGS=-ip -O3 -no-prec-div -xHost
> PMEMD_CC=icc
> PMEMD_COPTFLAGS=-ip -O3 -no-prec-div -xHost -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -DBINTRAJ
> PMEMD_FLIBSF=-Wl,--start-group
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_intel_lp64.a
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_sequential.a
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_core.a
> -Wl,--end-group -lpthread
> PMEMD_LD= ifort
> LDOUT= -o
>
>
> However, I seem to have a problem with pmemd.CUDA installation.
> I get the following error message after I type make install
>
>
> -L/usr/local/cuda-5.0/lib64 -L/usr/local/cuda-5.0/lib -lcurand -lcufft
> -lcudart ./cuda/cuda.a -L/usr/local/amber12/lib -L/usr/local/amber12/lib
> -lnetcdf -shared-intel -Wl,--start-group
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_intel_lp64.a
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_sequential.a
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_core.a
> -Wl,--end-group -lpthread
> ld: ./cuda/cuda.a(kNLRadixSort.o): undefined reference to symbol
> '__cxa_pure_virtual..CXXABI_1.3'
> ld: note: '__cxa_pure_virtual..CXXABI_1.3' is defined in DSO
> /usr/lib64/libstdc++.so.6 so try adding it to the linker command line
> /usr/lib64/libstdc++.so.6: could not read symbols: Invalid operation
> make[3]: *** [pmemd.cuda] Error 1
> make[3]: Leaving directory `/usr/local/amber12/src/pmemd/src'
> make[2]: *** [cuda] Error 2
> make[2]: Leaving directory `/usr/local/amber12/src/pmemd'
> make[1]: *** [cuda] Error 2
> make[1]: Leaving directory `/usr/local/amber12/src'
> make: *** [install] Error 2
>
>
> I guess the error is related to "/usr/lib64/libstdc++.so.6: could not read
> symbols: Invalid operation"
>
> Does anyone have a clue what might be going wrong with the installation?
>
>
> Best regards,
>
> Cenk Andac, M.S., Ph.D.
>
> Asst. Professor of Medical Pharmacology
> Department of Medical Pharmacology
> School of Medicine, Mevlana University, Konya
> Turkiye 42003
>
>
> Cell: +90-(536)-4813012
> E-Mail:cenk_andac.yahoo.com
> Web : http://med.mevlana.edu.tr/personel.asp?ID=1
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu May 16 2013 - 00:30:02 PDT
