Date: Mon, 5 Sep 2022 22:39:58 +0530
Dear Prof. Valentin,
Ok. I shall keep that in mind during the installation process. Thanks a lot.
With regards,
Satyajit Khatua,
Research Scholar,
Department of Chemistry,
IIT Kharagpur, Kharagpur-721302
On Mon, Sep 5, 2022 at 10:33 PM Rybenkov, Valentin V. <valya.ou.edu> wrote:
> There was also an issue with CUDA, we had to use the latest version,
> 11.3.1 or 11.4
>
>
>
> Valentin V. Rybenkov
> University of Oklahoma
> 101 Stephenson Parkway
> Norman, OK 73019
> Web: antibiotics.oucreate.com
>
>
>
> *From: *SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
> *Sent: *Monday, September 5, 2022 11:54 AM
> *To: *Rybenkov, Valentin V. <valya.ou.edu>; AMBER Mailing List
> <amber.ambermd.org>
> *Subject: *Re: [AMBER] Fwd: AMBER 22 installation with CUDA support
>
>
>
> Dear Prof. Valentin,
>
>
>
> Thank you for your valuable suggestions. Although the default CUDA version
> (CUDA 8.0) would suffice my need, It is mainly the GCC version that I am
> worried about. As AMBER 22 requires GCC 6 or above and CUDA 8.0 supports
> GCC 5.3 at max (as far as I know).
>
>
>
> So, I think I have to ask the system administrator about installing an
> updated version of the CUDA toolkit. Let's see if that solves the problem.
> Thanks again.
>
>
>
> With best regards,
>
> Satyajit Khatua
>
> *From:* Rybenkov, Valentin V. <valya.ou.edu>
> *Sent:* Monday, September 5, 2022 10:03:40 PM
> *To:* SATYAJIT KHATUA <satyajitkhatua09.gmail.com>; AMBER Mailing List <
> amber.ambermd.org>
> *Subject:* RE: [AMBER] Fwd: AMBER 22 installation with CUDA support
>
>
>
> Satyajit,
>
>
>
> I had similar problems installing Amber on a managed computer cluster.
> There were constant conflicts between preinstalled packages and what I was
> downloading. What worked for me was to use the preinstalled Cmake, OpenMPI,
> etc and forgo the installation of my own versions. Just use the module load
> xxx command. If you need a newer version of a soft than you have on your
> cluster, talk to your system administrator.
>
>
>
> Valentin
>
> Valentin V. Rybenkov
> University of Oklahoma
> 101 Stephenson Parkway
> Norman, OK 73019
> Web: antibiotics.oucreate.com
> <https://urldefense.com/v3/__http:/antibiotics.oucreate.com__;!!GNU8KkXDZlD12Q!8THuJ6xJt7KGt8FdTa8PTZUqumJrD9OYNOSKIMmsREphpfsem1ke6rnlHteeQu45K6osoicKcJSinZuCWpmTKOA$>
>
>
>
> *From: *SATYAJIT KHATUA via AMBER <amber.ambermd.org>
> *Sent: *Monday, September 5, 2022 11:03 AM
> *To: *AMBER Mailing List <amber.ambermd.org>
> *Subject: *[AMBER] Fwd: AMBER 22 installation with CUDA support
>
>
>
> As I have previously mailed only to Prof. Case, I am also floating the mail
> to the amber mailing list as well. Any help in this regard would be greatly
> appreciated.
>
> ---------- Forwarded message ---------
> From: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
> Date: Sun, Sep 4, 2022 at 9:57 PM
> Subject: Re: [AMBER] AMBER 22 installation with CUDA support
> To: David A Case <david.case.rutgers.edu>
>
>
> Dear Dr. Case,
>
> As you have suggested, using a newly installed CMake compiler I have
> successfully installed the GPU accelerated serial AMBER 22. But, the
> test.cuda.serial has encountered the attached error. However inspecting the
> log, I have seen that it is searching for a libcurand.so.8.0 file. But the
> installed CUDA version is 9.2. Thus there is ibcurand.so.9.2 file in my
> LD_LIBRARY_PATH. Do I have to unlink the root installed ibcurand.so.8.0?
>
> My .bashrc already contains the CUDA_HOME and its related LD_LIBRARY_PATH
> variables. What am I doing wrong here? Please advise.
>
> With regards,
> Satyajit Khatua,
> Research Scholar,
> Department of Chemistry,
> IIT Kharagpur, Kharagpur-721302
>
>
> On Sun, Sep 4, 2022 at 6:23 PM SATYAJIT KHATUA <satyajitkhatua09.gmail.com
> >
> wrote:
>
> > Hi,
> >
> > Thanks for the quick response. I will try to install some recent releases
> > on the cmake.org
> <https://urldefense.com/v3/__http:/cmake.org__;!!GNU8KkXDZlD12Q!8THuJ6xJt7KGt8FdTa8PTZUqumJrD9OYNOSKIMmsREphpfsem1ke6rnlHteeQu45K6osoicKcJSinZuCxKF8I-Y$>.
> Let's see if that works. I shall get back to you.
> >
> > Thanking you,
> >
> > Satyajit Khatua
> >
> > ------------------------------
> > *From:* David A Case <david.case.rutgers.edu>
> > *Sent:* Sunday, September 4, 2022 6:02:27 PM
> > *To:* SATYAJIT KHATUA <satyajitkhatua09.gmail.com>; AMBER Mailing List <
> > amber.ambermd.org>
> > *Subject:* Re: [AMBER] AMBER 22 installation with CUDA support
> >
> > On Sat, Sep 03, 2022, SATYAJIT KHATUA via AMBER wrote:
> > >
> > >I am installing AMBER22 in our departmental CentOS 7 cluster,...
> > >
> > >(message): Error generating
> >
> >
> >/home/satyajit/amber22_src/build/AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir//./cpptraj_cuda_routines_generated_GistCudaSetup.cu.omake[2]:
> > >***
> >
> >
> >[AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir/cpptraj_cuda_routines_generated_GistCudaSetup.cu.o]
> > >Error 1make[1]: ***
> >
> >
> >[AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir/all]
> > >Error 2make: *** [all] Error 2*
> >
> > Our Centos installation notes (https://ambermd.org/InstCentOS.php
> <https://urldefense.com/v3/__https:/ambermd.org/InstCentOS.php__;!!GNU8KkXDZlD12Q!8THuJ6xJt7KGt8FdTa8PTZUqumJrD9OYNOSKIMmsREphpfsem1ke6rnlHteeQu45K6osoicKcJSinZuCpqA_7kI$>
> )
> > suggests
> > installing cmake from the cmake.org
> <https://urldefense.com/v3/__http:/cmake.org__;!!GNU8KkXDZlD12Q!8THuJ6xJt7KGt8FdTa8PTZUqumJrD9OYNOSKIMmsREphpfsem1ke6rnlHteeQu45K6osoicKcJSinZuCxKF8I-Y$>
> website. Above is a cmake-error, but
> > I
> > don't remember seeing it reported by others; perhaps they were using a
> > different version of cmake.
> >
> > One workaround: during the CUDA build phase, add this to your run_cmake
> > script:
> >
> > -DDISABLE_TOOLS="cpptraj"
> >
> > ...good luck....dac
> >
> >
>
>
>
>
>
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