Dear David,
The installation seems to have finished well since all the tests have
passed.
thanks for your help.
==============================================================
cd gti/SC_Correction/complex/ && SC_CORR=2 ./Run.SC_NVT_MBAR DPFP
/home/exx/Downloads/amber20/test/cuda/gti/SC_Correction/complex
diffing md_SC_NVT_MBAR_SC_2.o.DPFP with md_SC_NVT_MBAR_SC_2.o
PASSED
==============================================================
make[3]: Leaving directory `/home/exx/Downloads/amber20/test/cuda'
make[2]: Leaving directory `/home/exx/Downloads/amber20/test'
make[2]: Entering directory `/home/exx/Downloads/amber20/test'
Finished CUDA test suite for Amber 20 at Thu Dec 10 22:04:41 +09 2020.
make[2]: Leaving directory `/home/exx/Downloads/amber20/test'
249 file comparisons passed
0 file comparisons failed
0 tests experienced errors
Test log file saved as
/home/exx/Downloads/amber20/logs/test_amber_cuda/2020-12-10_21-59-42.log
No test diffs to save!
make[1]: Leaving directory `/home/exx/Downloads/amber20/test'
(base) [exx.c107739 amber20]$
On Thu, Dec 10, 2020 at 9:18 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Dear David,
> I realized that I had set the DCUDA=TRUE only in one place in the
> run_cmake script.
> After changing the second occurrence to TRUE, I'm getting the following
> output.
> My current run_cmake script is pasted below in which I have DMPI=TRUE, but
> even then I get MPI OFF message.
> should I reset this to DMPI=FALSE?
> Now the make install is running for longer but is showing many warnings
> like the following.
>
> /home/exx/Downloads/amber20_src/src/pmemd/src/cuda/kCalculateLocalForces.cu(1109):
> warning: variable "GaMDTINBForceY" was declared but never referenced
> ptxas warning : Value of threads per SM for entry
> _Z32kCalcPMENBNrgVir32fswitch_kernelv is out of range. .minnctapersm will
> be ignored
> Thanks a lot for your help.
> -- Features:
> -- MPI: OFF
> -- OpenMP: OFF
> -- CUDA: ON
> -- NCCL: OFF
> -- Build Shared Libraries: ON
> -- Build GUI Interfaces: ON
> -- Build Python Programs: ON
> -- -Python Interpreter: Internal Miniconda (version 3.8)
> -- Build Perl Programs: ON
> -- Build configuration: RELEASE
> -- Target Processor: x86_64
> -- Build Documentation: OFF
> -- Sander Variants: normal LES API LES-API MPI LES-MPI
> -- Install location: /home/exx/Downloads/amber20/
> -- Installation of Tests: ON
>
> -- Compilers:
> -- C: GNU 4.8.5 (/usr/bin/gcc)
> -- CXX: GNU 4.8.5 (/usr/bin/g++)
> -- Fortran: GNU 4.8.5 (/usr/bin/gfortran)
>
> (base) [exx.c107739 build]$ cat run_cmake
> #!/bin/bash
>
> # This file gives some sample cmake invocations. You may wish to
> # edit some options that are chosen here.
>
> # For information on how to get cmake, visit this page:
> # https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Quick-Start
>
> # For information on common options for cmake, visit this page:
> # http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
>
> # (Note that you can change the value of CMAKE_INSTALL_PREFIX from what
> # is suggested below, but it cannot coincide with the amber20_src
> # folder.)
>
> AMBER_PREFIX=$(dirname $(dirname `pwd`))
>
> if [ `uname -s|awk '{print $1}'` = "Darwin" ]; then
>
> # For macOS:
>
> if [ -x /Applications/CMake.app/Contents/bin/cmake ]; then
> cmake=/Applications/CMake.app/Contents/bin/cmake
> else
> cmake=cmake
> fi
>
> $cmake $AMBER_PREFIX/amber20_src \
> -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 \
> -DCOMPILER=CLANG -DBLA_VENDOR=Apple \
> -DMPI=TRUE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
> -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE \
> 2>&1 | tee cmake.log
>
> else
>
> # Assume this is Linux:
>
> cmake $AMBER_PREFIX/amber20_src \
> -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 \
> -DCOMPILER=GNU \
> -DMPI=TURE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
> -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE \
> 2>&1 | tee cmake.log
>
> fi
>
> if [ ! -s cmake.log ]; then
> echo ""
> echo "Error: No cmake.log file created: you may need to edit run_cmake"
> exit 1
> fi
>
> echo ""
> echo "If the cmake build report looks OK, you should now do the following:"
> echo ""
> echo " make install"
> echo " source $AMBER_PREFIX/amber20/amber.sh"
> echo ""
> echo "Consider adding the last line to your login startup script, e.g.
> ~/.bashrc"
> echo ""
>
> On Thu, Dec 10, 2020 at 6:49 PM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Thu, Dec 10, 2020, Vaibhav Dixit wrote:
>>
>> >I'm getting the following message while trying to install GPU version of
>> >Amber20.
>> >The messages show that MPI, OpenMP and CUDA are OFF.
>>
>> Did you set -DCUDA=TRUE in your run_cmake script?
>>
>> I'm not sure what you mean by "the following message": no errors are
>> shown there. It might help if you post the arguments you are sending to
>> cmake, but it may be(?) that you didn't ask for the GPU version to be
>> built.
>>
>> ....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> P Please consider the environment before printing this e-mail
>
>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
_______________________________________________
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AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 10 2020 - 09:00:02 PST
