Re: [AMBER] CUDA version still not working

From: Fabian Glaser <>
Date: Thu, 18 Sep 2014 16:04:38 +0300

Hi Jason,

Here is the output of the command, everything looks OK, correct?

./configure -cuda -mpi gnu

Checking for updates...
NoInternetAccess: Cannot connect to
Checking for available patches online. This may take a few seconds...
Check for updates failed.
Searching for python2... Found python2.6: /usr/bin/python2.6

Obtaining the gnu suite version:
      gcc -v
The version is 4.4.7

Testing the gcc compiler:
     gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c

Testing the gfortran compiler:
     gfortran -O0 -o testp testp.f

Testing mixed C/Fortran compilation:
     gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
     gfortran -O0 -c -o testp.f.o testp.f
     gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w

Testing pointer size:
     gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size test_pointer_size.c
Detected 64 bit operating system.

Testing flex:./configure2: line 1848: flex: command not found

Warning: Unable to run flex; this is recommended for NAB
Please check your PATH, or install the program

We will try to soldier on with precompiled files

Configuring NetCDF (may be time-consuming)...

    NetCDF configure succeeded.

Checking for zlib: OK

Checking for libbz2: OK
Skipping configuration of FFTW3
The configuration file, config.h, was successfully created.
The next step is to type 'make install'
Cleaning the src directories. This may take a few moments.
Configure complete.

Fabian Glaser, PhD

Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU

The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
Tel: +972 4 8293701
Fax: +972 4 8225153

On Sep 18, 2014, at 2:40 PM, Jason Swails <> wrote:

> On Thu, 2014-09-18 at 11:39 +0300, Fabian Glaser wrote:
>> Hi all,
>> We have updated all the following drivers on ReadHat 6.4 (see below),
>> and still running pmemd.cuda I get a different error this time, sander
>> works normally:
>> -bash-4.1$ pmemd.cuda -O -i -p RIT_6mol_h_wat.prmtop -c
>> RIT_6mol_h_wat_eq5.rst -ref RIT_6mol_h_wat_eq5.rst -o
>> RIT_6mol_h_wat_md1.out -x RIT_6mol_h_wat_md1.mdcrd -r
>> RIT_6mol_h_wat_md1.rst
>> pmemd.cuda: error while loading shared libraries:
>> cannot open shared object file: No such file or directory
>> Is this something known to you?
>> Looking into different forums, our technical people don't find the
>> specific library....
> The library is part of the CUDA toolkit distribution.
> If you run "./configure -cuda gnu", the end of the configure step you
> should see a message like this:
> --------------------------------------------------------------------------------
> Environment resource files are provided to set the proper environment
> variables to use AMBER and AmberTools.
> If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
> /home/swails/build_amber/amber/ file in your shell. Consider adding the line
> test -f /home/swails/build_amber/amber/ && source /home/swails/build_amber/amber/
> to your startup file (e.g., ~/.bashrc)
> If you use a C shell (e.g., csh, tcsh), source the
> /home/swails/build_amber/amber/amber.csh file in your shell. Consider adding the line
> test -f /home/swails/build_amber/amber/amber.csh && source /home/swails/build_amber/amber/amber.csh
> to your startup file (e.g., ~/.cshrc)
> If you have not already done so, you may need to add /opt/cuda/5.5/lib
> and/or /opt/cuda/5.5/lib64 to LD_LIBRARY_PATH using the command
> export LD_LIBRARY_PATH="/opt/cuda/5.5/lib:${LD_LIBRARY_PATH}" (bash, sh)
> setenv LD_LIBRARY_PATH "/opt/cuda/5.5/lib:${LD_LIBRARY_PATH}" (tcsh, csh)
> --------------------------------------------------------------------------------
> The last piece of advice -- namely adding $CUDA_HOME/lib and/or
> $CUDA_HOME/lib64 to your LD_LIBRARY_PATH -- is the root cause of your
> error. On my computer, CUDA_HOME happens to be set to /opt/cuda/5.5.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

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Received on Thu Sep 18 2014 - 06:30:04 PDT
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