Seawulf Items Needed

List of Items needed

• python 2.7 (create module)
  • • numpy
    • matplotlib
    • scipy
    • ipython
    • pandas
    • cython
    • mpi4py
    • notebook
    • RDKit
      • We haven't been using this RDK Toolkit, but it was recommended/used by Michael Gilson and other group, and it seems to be useful and powerful, here's a link to the installation guide page http://www.rdkit.org/docs/Install.html
• X11 forwarding
• Increase GPU queue max walltime to 12hrs

AMBER CUDA builds

AMBER + CUDA7.5 and 8.0 via GCC compilers: OK
module loaded

1) torque/6.0.2  2) cuda75/toolkit/7.5.18

AMBER + CUDA7.5 or 8.0 via intel compilers: Fails
modules loaded

   1) torque/6.0.2                    3) intel/mkl/64/2017/0.098         5) cuda75/toolkit/7.5.18
  2) intel/compiler/64/2017/17.0.0   4) intel/mpi/64/2017/0.098 

configure -cuda -noX11 --with-python (path to python) intel; fails with the following error

/cm/shared/apps/cuda75/toolkit/7.5.18/bin/nvcc -c -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_50,code=sm_50 -gencode arch=compute_52,code=sm_52 -gencode arch=compute_53,code=sm_53 -o core_kernels.o core_kernels.cu In file included from /cm/shared/apps/cuda75/toolkit/7.5.18/bin/..//include/driver_types.h:70:0, from /cm/shared/apps/cuda75/toolkit/7.5.18/bin/..//include/builtin_types.h:59, from /cm/shared/apps/cuda75/toolkit/7.5.18/bin/..//include/cuda_runtime.h:84, from <command-line>:0: /cm/shared/apps/intel/compilers_and_libraries/2017.0.098/compiler/include/limits.h:36:54: error: missing binary operator before token "("defined(__has_include_next) && __has_include_next(<limits.h>) In file included from /cm/shared/apps/cuda75/toolkit/7.5.18/bin/..//include/math_functions.h:8791:0, from /cm/shared/apps/cuda75/toolkit/7.5.18/bin/..//include/common_functions.h:224, from /cm/shared/apps/cuda75/toolkit/7.5.18/bin/..//include/cuda_runtime.h:112, from <command-line>:0: /cm/shared/apps/intel/compilers_and_libraries/2017.0.098/compiler/include/math.h:108:3: error: #error "This Intel <math.h> is for use with only the Intel compilers!" # error "This Intel <math.h> is for use with only the Intel compilers!"