Thank You for your reply. I do the same task as you mentioned. Then I test
the pemmd.cuda.MPI. I got the following message.
make[3]: Leaving directory `/home/srabani/Downloads/amber18/test/cuda'
make[2]: Leaving directory `/home/srabani/Downloads/amber18/test'
*200 file comparisons passed1 file comparisons failed (0 ignored)0 tests
experienced errors*
Test log file saved as
/home/srabani/Downloads/amber18/logs/test_amber_cuda_parallel/2024-03-05_09-47-42.log
Test diffs file saved as
/home/srabani/Downloads/amber18/logs/test_amber_cuda_parallel/2024-03-05_09-47-42.diff
*make[1]: *** [test.cuda.parallel] Error 1make[1]: Leaving directory
`/home/srabani/Downloads/amber18/test'make: [test.cuda_parallel] Error 2
(ignored)*
*I think the error appears due to not cuda parallelization in the system.*
On Sun, Mar 3, 2024 at 7:30 PM Hector A. Baldoni <hbaldoni.unsl.edu.ar>
wrote:
> Dear Dulal,
>
> It looks like the error is related to the removal of a write-protected
> file in the NetCDF library. Here are a few steps you can take to resolve
> this issue:
>
> 1. **Check File Permissions:**
> Make sure that you have the necessary permissions to modify or delete
> files in the specified directory. You can use the `ls -l` command to
> check the permissions of the file and the directory.
> ls -l /home/srabani/Downloads/amber18/lib/libnetcdf.a
> If the file is write-protected, you might need to change its
> permissions using the `chmod` command:
> chmod +w /home/srabani/Downloads/amber18/lib/libnetcdf.a
>
> 2. **Re-run the Configuration:**
> After ensuring that you have the required permissions, you can try
> running the `./configure` command again:
> ./configure -cuda -mpi gnu
>
> 3. **Clean and Rebuild:**
> If the issue persists, you may want to clean the build directory and
> start the configuration and compilation process from scratch. Use the
> following commands:
> make clean
> ./configure -cuda -mpi gnu
> make
>
> 4. **Manual Removal (if necessary):**
> If all else fails, you can manually remove the write-protected file
> and then run the configuration again. Please be cautious when using the
> `rm` command, as it will permanently delete files.
> rm -f /home/srabani/Downloads/amber18/lib/libnetcdf.a
> ./configure -cuda -mpi gnu
>
> 5. **Check System Dependencies:**
> Ensure that you have all the required dependencies installed on your
> system, especially those related to NetCDF. You may need to install the
> development version of the NetCDF library.
> sudo apt-get install libnetcdf-dev
>
>
> Greeting,
> Hector
>
> El 2024-03-03 05:16, Dulal Mondal via AMBER escribió:
> > Please response.
> >
> > On Sat, 2 Mar, 2024, 12:29 pm Dulal Mondal, <
> > babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
> >
> >> Dear Experts,
> >>
> >> I am trying to compile amber18 cuda.MPI. I type the following command
> >>
> >> ./configure -cuda -mpi gnu
> >>
> >> But it shows the following message.
> >> Testing flex:OK
> >>
> >> Testing bison:
> >> OK
> >>
> >>
> >>
> >>
> >>
> >> *Checking NetCDF... Using bundled NetCDF library. NetCDF must be
> >> rebuilt./bin/rm: remove write-protected regular file
> >> ‘/home/srabani/Downloads/amber18/lib/libnetcdf.a’? *
> >> How do I solve this problem?
> >>
> >> --
> >> *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
>
> --
> --------------------------------------
> Dr. Hector A. Baldoni
> Profesor Titular (FQByF-UNSL)
> Investigador Adjunto (IMASL-CONICET)
> Area de Quimica General e Inorganica
> Universidad Nacional de San Luis
> Chacabuco 917 (D5700BWS)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.:+54-(0)266-4520300 ext. 6157
> --------------------------------------
> 2024 - Año de la Defensa de la Vida, la Libertad y la Propiedad.
> Decreto 55/2024 GN
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Mon Mar 04 2024 - 21:30:01 PST
