Hello Amber users
I have extracted AmberTools 19 and Amber14 and put them in folder Amber18
in /usr/local directory.
My graphic cart is : GF108 [GeForce GT 440] and I have installed nvidia
driver (NVIDIA-SMI 390.116, Driver Version: 390.116) and cuda-9.0 toolkit
software (Cuda compilation tools, release 9.0, V9.0.176) in /usr/local
directory as superviser user and ./deviceQuery (in
/usr/local/cuda/samples/bin/x86_64/linux/release) command works:
deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 9.1, CUDA Runtime
Version = 9.0, NumDevs = 1
Result = PASS
I have to install cuda-9.0 , because my graphic cart and my nvidia driver
only work with cuda-9.0.
my Ubnutu is 18.04 (4.15.0-55-generic) and gcc version is 6.5.0 (gcc
(Ubuntu 6.5.0-2ubuntu1~18.04) 6.5.0 20181026) and my gfortran is 7.4.0 (GNU
Fortran (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0).
I set environmental variables as follows:
test -f /usr/local/amber18/amber.sh
source /usr/local/amber18/amber.sh
export AMBERHOME=/usr/local/amber18
export CUDA_HOME=/usr/local/cuda-9.0
export PATH=/usr/local/cuda-9.0/bin${PATH:+:${PATH}}
export LD_LIBRARY_PATH="/usr/local/cuda-9.0/lib64:${LD_LIBRARY_PATH}"
in .bashrc file in root directory and source them and also inserted thses
variables in linux terminal (echo $CUDA_HOME says: /usr/local/cuda-9.0).
I have installed MPI version of amber and sander.MPI works, I want to
install GPU version of Amber and I performed "make clean" and "./configure
-cuda gnu" without error in Amber18 directory.
When I perform "make install" as superviser, it says :
mv cpptraj.cuda "/usr/local/amber18/bin"
make[4]: Leaving directory '/usr/local/amber18/AmberTools/src/cpptraj/src'
make[3]: Leaving directory '/usr/local/amber18/AmberTools/src/cpptraj'
make[2]: Leaving directory '/usr/local/amber18/AmberTools/src'
AmberTools serial CUDA install complete.
make[1]: Leaving directory '/usr/local/amber18/AmberTools/src'
make[1]: Entering directory '/usr/local/amber18/src'
make[1]: *** No rule to make target 'cuda_serial', needed by 'install'.
Stop.
make[1]: Leaving directory '/usr/local/amber18/src'
Makefile:7: recipe for target 'install' failed
make: *** [install] Error 2
and pmemd.cuda does not work.
Would you please tell me how can I solve this problem.
Thank you very much.
Dr. Karim Mahnam
Associate Professor in Shahrkord University
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Received on Thu Aug 01 2019 - 04:00:02 PDT
