Difference between revisions of "Seawulf Items Needed"
From Rizzo_Lab
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== List of Items needed == | == List of Items needed == | ||
*python 2.7 (create module) | *python 2.7 (create module) | ||
| − | ** | + | ***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 | * X11 forwarding | ||
*Increase GPU queue max walltime to 12hrs | *Increase GPU queue max walltime to 12hrs | ||
| − | + | ===AMBER CUDA builds=== | |
| − | AMBER + CUDA7.5 | + | AMBER + '''CUDA7.5 or 8.0''' via GCC compilers: OK<br> |
| − | AMBER + CUDA7.5 intel compilers | + | module loaded |
| − | + | {| | |
| − | /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, | + | <pre>1) torque/6.0.2 2) cuda75/toolkit/7.5.18</pre> |
| + | |} | ||
| + | AMBER + '''CUDA7.5 or 8.0''' via intel compilers: Fails<br> | ||
| + | modules loaded | ||
| + | {| | ||
| + | <pre> | ||
| + | 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 </pre> | ||
| + | |} | ||
| + | {| | ||
| + | configure -cuda -noX11 --with-python (path to python) intel; fails with the following error | ||
| + | |<pre>/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/builtin_types.h:59, | ||
from /cm/shared/apps/cuda75/toolkit/7.5.18/bin/..//include/cuda_runtime.h:84, | from /cm/shared/apps/cuda75/toolkit/7.5.18/bin/..//include/cuda_runtime.h:84, | ||
from <command-line>:0: | 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 "(" | + | /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, | 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/common_functions.h:224, | ||
| Line 25: | Line 37: | ||
from <command-line>:0: | 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!" | /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!" | + | # error "This Intel <math.h> is for use with only the Intel compilers!"</pre> |
| + | | | ||
| + | |} | ||
Latest revision as of 13:36, 9 March 2017
List of Items needed
- python 2.7 (create module)
- 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 or 8.0 via GCC compilers: OK
module loaded
AMBER + CUDA7.5 or 8.0 via intel compilers: Fails
modules loaded
/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!"
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