I couldn't find any error in your log file.
Can you write the exact error?
Best,
Masoud
________________________________
From: Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in>
Sent: Tuesday, July 30, 2024 13:33
To: Masoud Keramati <keramati.m.northeastern.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] amber24 cuda installation error
Thank you for your reply. Now my run_cmake file is:
# Assume this is Linux:
cmake $AMBER_PREFIX/amber24_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
-DCOMPILER=GNU \
-DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=FALSE -DFORCE_DISABLE_LIBS=perlmol \
-DDOWNLOAD_MINICONDA=TRUE \
2>&1 | tee cmake.log
Again compilation error.
On Tue, Jul 30, 2024 at 8:07 PM Masoud Keramati <keramati.m.northeastern.edu<mailto:keramati.m.northeastern.edu>> wrote:
Keep miniconda flag as TRUE.
Best,
Masoud
Get Outlook for iOS<
https://aka.ms/o0ukef>
________________________________
From: Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in<mailto:babunmondal.chem.kgpian.iitkgp.ac.in>>
Sent: Tuesday, July 30, 2024 2:20:57 AM
To: Masoud Keramati <keramati.m.northeastern.edu<mailto:keramati.m.northeastern.edu>>
Cc: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: Re: [AMBER] amber24 cuda installation error
Thank you for your reply.
Now my run_cmake file is like below.
Assume this is Linux:
cmake $AMBER_PREFIX/amber24_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
-DCOMPILER=GNU \
-DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=FALSE -DFORCE_DISABLE_LIBS=perlmol \
-DDOWNLOAD_MINICONDA=FALSE \
2>&1 | tee cmake.log
But it does not compile. I attached the related log files.
On Mon, Jul 29, 2024 at 11:00 PM Masoud Keramati <keramati.m.northeastern.edu<mailto:keramati.m.northeastern.edu>> wrote:
Try adding this:
-DFORCE_DISABLE_LIBS=perlmol
Best,
Masoud
________________________________
From: Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in<mailto:babunmondal.chem.kgpian.iitkgp.ac.in>>
Sent: Monday, July 29, 2024 12:05
To: Masoud Keramati <keramati.m.northeastern.edu<mailto:keramati.m.northeastern.edu>>; AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: Re: [AMBER] amber24 cuda installation error
Dear Masoud and AMBER,
I set -DDOWNLOAD_MINICONDA=TRUE. My run cmake file is below.
Assume this is Linux:
cmake $AMBER_PREFIX/amber24_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
-DCOMPILER=GNU \
-DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE \
2>&1 | tee cmake.log
The error found in the log files are attached below (compilation error)
On Sat, Jul 27, 2024 at 8:23 PM Masoud Keramati <keramati.m.northeastern.edu<mailto:keramati.m.northeastern.edu>> wrote:
As far as I know, DDOWNLOAD_MINICONDA flag should be TRUE. There are lots of missing libraries.
Best,
Masoud Keramati
PhD Candidate, Bioengineering, Northeastern University
________________________________
From: Dulal Mondal via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>>
Sent: Friday, July 26, 2024 23:55
To: Goetz, Andreas <awgoetz.ucsd.edu<mailto:awgoetz.ucsd.edu>>; David A Case <dacase1.gmail.com<mailto:dacase1.gmail.com>>
Cc: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: Re: [AMBER] amber24 cuda installation error
Thank You for your reply. My run_cmake file is like below.
Assume this is Linux:
cmake $AMBER_PREFIX/amber24_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
-DCOMPILER=GNU \
-DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=FALSE \
2>&1 | tee cmake.log
But it shows that the configuration is incomplete.
then I type ./run_cmake
GNU compiler version are
Compilers:
-- C: GNU 11.4.0 (/usr/bin/gcc)
-- CXX: GNU 11.4.0 (/usr/bin/g++)
-- Fortran: GNU 11.4.0 (/usr/bin/gfortran)
cmake version Starting configuration of Amber version 24.0.0...
-- CMake Version: 3.22.1
cuda version Found CUDA: /usr (found version "11.5")
-- CUDA version 11.5 detected
There are some warning messages during compilation: CMake Warning at
cmake/CudaConfig.cmake:168 (message):
Cannot find the NVidia Management Library (libnvidia-ml) in your CUDA
toolkit. mdgx.cuda will not be built.
I uploaded the related file.
On Sat, Jul 27, 2024 at 2:43 AM Goetz, Andreas <awgoetz.ucsd.edu<mailto:awgoetz.ucsd.edu>> wrote:
> I am not an expert, but those who are likely need to know what version of
>
> compilers (both for CPU and CUDA) that you are using.
>
>
> In addition to compiler versions please also include the cmake command you
> used.
>
> All the best,
> Andy
> —
> Dr. Andreas W. Goetz
> Associate Research Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email: agoetz.sdsc.edu<mailto:agoetz.sdsc.edu>
> Web: https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.awgoetz.de%2F&data=05%7C02%7Ckeramati.m%40northeastern.edu%7C9d8b81bea23c461aa33a08dcadf00a8f%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638576493704305841%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Qz2HcHXnNncbYMNLeMxHOmD5gPkTS9Iw7kA4hxbYmE0%3D&reserved=0<http://www.awgoetz.de/>
>
> On Jul 26, 2024, at 11:21 AM, David A Case via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>>
> wrote:
>
> On Fri, Jul 26, 2024, Dulal Mondal via AMBER wrote:
>
> Dear Experts,
>
>
> I am not an expert, but those who are likely need to know what version of
> compilers (both for CPU and CUDA) that you are using.
>
> ...dac
>
> I am trying to install pmemd.cuda (amber24). It is configured properly. But
> during installation step it stops at 54 percent.
>
> [ 54%] Building NVCC (Device) object
>
> AmberTools/src/quick/src/cuda/CMakeFiles/quick_cuda_kernels.dir/quick_cuda_kernels_generated_gpu_get2e.cu.o
>
> /usr/include/c++/11/bits/std_function.h:530:146: note: ‘_ArgTypes’
> CMake Error at
> quick_cuda_kernels_generated_gpu_get2e_grad_ffff.cu.o.RELEASE.cmake:278
> (message):
> Error generating file
>
>
> /home/srabani/Downloads/amber24_src/build/AmberTools/src/quick/src/cuda/CMakeFiles/quick_cuda_kernels.dir//./quick_cuda_kernels_generated_gpu_get2e_grad_ffff.cu.o
>
>
> make[2]: ***
>
> [AmberTools/src/quick/src/cuda/CMakeFiles/quick_cuda_kernels.dir/build.make:112:
>
> AmberTools/src/quick/src/cuda/CMakeFiles/quick_cuda_kernels.dir/quick_cuda_kernels_generated_gpu_get2e_grad_ffff.cu.o]
> Error 1
> make[1]: *** [CMakeFiles/Makefile2:7556:
> AmberTools/src/quick/src/cuda/CMakeFiles/quick_cuda_kernels.dir/all] Error
> 2
> make: *** [Makefile:156: all] Error 2
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
>
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber__%3B!!Mih3wA!GcdgGZcGtg6tAhS3wbVQUHoNEQ8CVOHa2wxdL8Mii04jc2K8tBAqWpjRDDQc19dd_zQnQ9Dhnj2iRg%24&data=05%7C02%7Ckeramati.m%40northeastern.edu%7C9d8b81bea23c461aa33a08dcadf00a8f%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638576493704315120%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=W90csIZCbS5pKRmgdcT5pnX3RHbYhJvZbhtmD6f1mYg%3D&reserved=0<https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!Mih3wA!GcdgGZcGtg6tAhS3wbVQUHoNEQ8CVOHa2wxdL8Mii04jc2K8tBAqWpjRDDQc19dd_zQnQ9Dhnj2iRg$>
>
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
--
With regards,
Dulal Mondal,
Research Scholar,
Department of Chemistry,
IIT Kharagpur, Kharagpur 721302.
--
With regards,
Dulal Mondal,
Research Scholar,
Department of Chemistry,
IIT Kharagpur, Kharagpur 721302.
--
With regards,
Dulal Mondal,
Research Scholar,
Department of Chemistry,
IIT Kharagpur, Kharagpur 721302.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 30 2024 - 11:00:03 PDT
