Here are my notes to install Amber24 on Ubuntu24 and MX Linux 23.
Best wishes
Gert Kruger
On Tue, 2024-07-30 at 23:03 +0530, Dulal Mondal via AMBER wrote:
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>
wrote:
> Keep miniconda flag as TRUE.
>
> Best,
> Masoud
>
> Get Outlook for iOS <https://aka.ms/o0ukef<https://url.za.m.mimecastprotect.com/s/p61dCzmlY0F6EJl9uBH7tn?domain=aka.ms>>
> ------------------------------
> *From:* Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in>
> *Sent:* Tuesday, July 30, 2024 2:20:57 AM
> *To:* Masoud Keramati <keramati.m.northeastern.edu>
> *Cc:* AMBER Mailing List <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> wrote:
>
> Try adding this:
> -DFORCE_DISABLE_LIBS=perlmol
>
>
> Best,
>
> Masoud
>
> ------------------------------
> *From:* Dulal Mondal <babunmondal.chem.kgpian.iitkgp.ac.in>
> *Sent:* Monday, July 29, 2024 12:05
> *To:* Masoud Keramati <keramati.m.northeastern.edu>; AMBER Mailing List <
> 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> 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>
> *Sent:* Friday, July 26, 2024 23:55
> *To:* Goetz, Andreas <awgoetz.ucsd.edu>; David A Case <dacase1.gmail.com>
> *Cc:* AMBER Mailing List <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> 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
> > 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<https://url.za.m.mimecastprotect.com/s/zCIXCAnOKyf4B7y2COP7W7?domain=nam12.safelinks.protection.outlook.com>
> <http://www.awgoetz.de/<https://url.za.m.mimecastprotect.com/s/sZmqCBgE9zSj0EQBt73WQQ?domain=awgoetz.de>>
> >
> > On Jul 26, 2024, at 11:21 AM, David A Case via AMBER <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
> >
> >
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> >
> >
>
> --
> *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.*
>
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Received on Tue Jul 30 2024 - 11:00:03 PDT
