jamesdalg commented 8 months ago

I am attempting to install openmm-tensorflow and am getting a prompt in ccmake about the build type and the CUDA_SDK_ROOT_DIR.

                                                     Page 1 of 1
 **CMAKE_BUILD_TYPE**                *
 CMAKE_INSTALL_PREFIX             /usr/local/openmm
 CUDA_HOST_COMPILER               /usr/bin/cc
 **CUDA_SDK_ROOT_DIR**                CUDA_SDK_ROOT_DIR-NOTFOUND
 CUDA_TOOLKIT_ROOT_DIR            /usr/local/cuda-12.2
 CUDA_USE_STATIC_CUDA_RUNTIME     ON
 CUDA_rt_LIBRARY                  /usr/lib/x86_64-linux-gnu/librt.a
 NN_BUILD_CUDA_LIB                ON
 NN_BUILD_OPENCL_LIB              ON
 NN_BUILD_PYTHON_WRAPPERS         ON
 OPENCL_INCLUDE_DIR               /usr/include
 OPENCL_LIBRARY                   /usr/lib/x86_64-linux-gnu/libOpenCL.so
 OPENMM_DIR                       /usr/local/openmm
 PYTHON_EXECUTABLE                /home/jd/mambaforge/envs/openmmtensorflow/bin/python
 SWIG_EXECUTABLE                  /usr/bin/swig
 TENSORFLOW_DIR                   /usr/local

I have configured my environment as the following:

(openmmtensorflow) jd@oban:/code/openmm/openmm_plugins/openmm-tensorflow/build$ conda env export
name: openmmtensorflow
channels:
  - nvidia  - conda-forge
  - omnia
  - bioconda
  - defaults
  - anaconda
  - hcc
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - absl-py=2.0.0=pyhd8ed1ab_0
  - aiohttp=3.9.1=py311h459d7ec_0
  - aiosignal=1.3.1=pyhd8ed1ab_0
  - astunparse=1.6.3=pyhd8ed1ab_0
  - attrs=23.2.0=pyh71513ae_0
  - blinker=1.7.0=pyhd8ed1ab_0
  - brotli-python=1.1.0=py311hb755f60_1
  - bzip2=1.0.8=hd590300_5
  - c-ares=1.25.0=hd590300_0
  - ca-certificates=2023.11.17=hbcca054_0
  - cached-property=1.5.2=hd8ed1ab_1
  - cached_property=1.5.2=pyha770c72_1
  - cachetools=5.3.2=pyhd8ed1ab_0
  - certifi=2023.11.17=pyhd8ed1ab_0
  - cffi=1.16.0=py311hb3a22ac_0
  - charset-normalizer=3.3.2=pyhd8ed1ab_0
  - click=8.1.7=unix_pyh707e725_0
  - cryptography=41.0.7=py311hcb13ee4_1
  - cuda-version=11.7=h67201e3_2
  - cudatoolkit=11.7.0=hd8887f6_10
  - cudnn=8.8.0.121=hcdd5f01_4
  - flatbuffers=23.5.26=h59595ed_1
  - frozenlist=1.4.1=py311h459d7ec_0
  - gast=0.5.4=pyhd8ed1ab_0
  - giflib=5.2.1=h0b41bf4_3
  - google-auth=2.26.1=pyhca7485f_0
  - google-auth-oauthlib=1.0.0=pyhd8ed1ab_1
  - google-pasta=0.2.0=pyh8c360ce_0
  - grpcio=1.54.3=py311hcafe171_0
  - h5py=3.10.0=nompi_py311hebc2b07_101
  - hdf5=1.14.3=nompi_h4f84152_100
  - icu=73.2=h59595ed_0
  - idna=3.6=pyhd8ed1ab_0
  - importlib-metadata=7.0.1=pyha770c72_0
  - keras=2.13.1=pyhd8ed1ab_0
  - keyutils=1.6.1=h166bdaf_0
  - krb5=1.21.2=h659d440_0
  - ld_impl_linux-64=2.40=h41732ed_0
  - libabseil=20230125.3=cxx17_h59595ed_0
  - libaec=1.1.2=h59595ed_1
  - libblas=3.9.0=20_linux64_openblas
  - libcblas=3.9.0=20_linux64_openblas
  - libcurl=8.5.0=hca28451_0
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=hd590300_2
  - libexpat=2.5.0=hcb278e6_1
  - libffi=3.4.2=h7f98852_5
  - libgcc-ng=13.2.0=h807b86a_3
  - libgfortran-ng=13.2.0=h69a702a_3
  - libgfortran5=13.2.0=ha4646dd_3
  - libgomp=13.2.0=h807b86a_3
  - libgrpc=1.54.3=hb20ce57_0
  - libjpeg-turbo=3.0.0=hd590300_1
  - liblapack=3.9.0=20_linux64_openblas
  - libnghttp2=1.58.0=h47da74e_1
  - libnsl=2.0.1=hd590300_0
  - libopenblas=0.3.25=pthreads_h413a1c8_0
  - libpng=1.6.39=h753d276_0
  - libprotobuf=3.21.12=hfc55251_2
  - libsqlite=3.44.2=h2797004_0
  - libssh2=1.11.0=h0841786_0
  - libstdcxx-ng=13.2.0=h7e041cc_3
  - libuuid=2.38.1=h0b41bf4_0
  - libxcrypt=4.4.36=hd590300_1
  - libzlib=1.2.13=hd590300_5
  - markdown=3.5.1=pyhd8ed1ab_0
  - markupsafe=2.1.3=py311h459d7ec_1
  - multidict=6.0.4=py311h459d7ec_1
  - nccl=2.19.4.1=h0800d71_0
  - ncurses=6.4=h59595ed_2
  - numpy=1.26.3=py311h64a7726_0
  - oauthlib=3.2.2=pyhd8ed1ab_0
  - ocl-icd=2.3.1=h7f98852_0
  - ocl-icd-system=1.0.0=1
  - openmm=8.1.0=py311h6f6ebe4_1
  - openssl=3.2.0=hd590300_1
  - opt_einsum=3.3.0=pyhc1e730c_2
  - packaging=23.2=pyhd8ed1ab_0
  - pip=23.3.2=pyhd8ed1ab_0
  - protobuf=4.21.12=py311hcafe171_0
  - pyasn1=0.5.1=pyhd8ed1ab_0
  - pyasn1-modules=0.3.0=pyhd8ed1ab_0
  - pycparser=2.21=pyhd8ed1ab_0
  - pyjwt=2.8.0=pyhd8ed1ab_0
  - pyopenssl=23.3.0=pyhd8ed1ab_0
  - pysocks=1.7.1=pyha2e5f31_6
  - python=3.11.7=hab00c5b_1_cpython
  - python-flatbuffers=23.5.26=pyhd8ed1ab_0
  - python_abi=3.11=4_cp311
  - pyu2f=0.1.5=pyhd8ed1ab_0
  - re2=2023.03.02=h8c504da_0
  - readline=8.2=h8228510_1
  - requests=2.31.0=pyhd8ed1ab_0
  - requests-oauthlib=1.3.1=pyhd8ed1ab_0
  - rsa=4.9=pyhd8ed1ab_0
  - scipy=1.11.4=py311h64a7726_0
  - setuptools=69.0.3=pyhd8ed1ab_0
  - six=1.16.0=pyh6c4a22f_0
  - snappy=1.1.10=h9fff704_0
  - tensorboard=2.13.0=pyhd8ed1ab_0
  - tensorboard-data-server=0.7.0=py311h63ff55d_1
  - tensorflow=2.13.1=cuda112py311h693fce6_1
  - tensorflow-base=2.13.1=cuda112py311h8bdbb6c_1
  - tensorflow-estimator=2.13.1=cuda112py311h0d913ca_1
  - termcolor=2.4.0=pyhd8ed1ab_0
  - tk=8.6.13=noxft_h4845f30_101
  - typing_extensions=4.5.0=pyha770c72_0
  - tzdata=2023d=h0c530f3_0
  - urllib3=2.1.0=pyhd8ed1ab_0
  - werkzeug=3.0.1=pyhd8ed1ab_0
  - wheel=0.42.0=pyhd8ed1ab_0
  - wrapt=1.16.0=py311h459d7ec_0
  - xz=5.2.6=h166bdaf_0
  - yarl=1.9.3=py311h459d7ec_0
  - zipp=3.17.0=pyhd8ed1ab_0
  - zlib=1.2.13=hd590300_5
  - zstd=1.5.5=hfc55251_0
prefix: /home/jd/mambaforge/envs/openmmtensorflow

What precisely needs to be set in these two fields? CMAKE_BUILD_TYPE CUDA_SDK_ROOT_DIR

To clarify, I have created a build dir in /code/openmm/openmm_plugins/openmm-tensorflow/build after just cloning the repository.

jamesdalg commented 8 months ago

Here is my current nvidia-smi output:

(openmmtensorflow) jd@oban:/code/openmm/openmm_plugins/openmm-tensorflow/build$ nvidia-smi
Wed Jan 10 13:54:09 2024       
+---------------------------------------------------------------------------------------+
| NVIDIA-SMI 535.104.05             Driver Version: 535.104.05   CUDA Version: 12.2     |
|-----------------------------------------+----------------------+----------------------+
| GPU  Name                 Persistence-M | Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp   Perf          Pwr:Usage/Cap |         Memory-Usage | GPU-Util  Compute M. |
|                                         |                      |               MIG M. |
|=========================================+======================+======================|
|   0  NVIDIA RTX A5000               On  | 00000000:17:00.0 Off |                  Off |
| 30%   33C    P8              25W / 230W |    851MiB / 24564MiB |      0%      Default |
|                                         |                      |                  N/A |
+-----------------------------------------+----------------------+----------------------+
|   1  NVIDIA RTX A5000               On  | 00000000:73:00.0  On |                  Off |
| 30%   56C    P0              67W / 230W |   3753MiB / 24564MiB |     35%      Default |
|                                         |                      |                  N/A |
+-----------------------------------------+----------------------+----------------------+

+---------------------------------------------------------------------------------------+
| Processes:                                                                            |
|  GPU   GI   CI        PID   Type   Process name                            GPU Memory |
|        ID   ID                                                             Usage      |
|=======================================================================================|
|    0   N/A  N/A      4358      G   /usr/lib/xorg/Xorg                            4MiB |
|    0   N/A  N/A     34246      C   ...s/ovito-pro-3.10.0-x86_64/bin/ovito      834MiB |
|    1   N/A  N/A      4358      G   /usr/lib/xorg/Xorg                         1521MiB |
|    1   N/A  N/A      4537      G   /usr/bin/gnome-shell                        287MiB |
|    1   N/A  N/A     34246      G   ...s/ovito-pro-3.10.0-x86_64/bin/ovito       56MiB |
|    1   N/A  N/A     94411      G   coolercontrol                               198MiB |
|    1   N/A  N/A     97986      G   ...irefox/3600/usr/lib/firefox/firefox      351MiB |
|    1   N/A  N/A    257098      G   ...sion,SpareRendererForSitePerProcess      331MiB |
|    1   N/A  N/A    257100      G   ...ures=SpareRendererForSitePerProcess      471MiB |
|    1   N/A  N/A    257286      G   ...7145292,18175410111797470196,262144      147MiB |
+---------------------------------------------------------------------------------------+

peastman commented 8 months ago

Set CMAKE_BUILD_TYPE to Release.

Set CUDA_SDK_ROOT_DIR to wherever the CUDA toolkit is installed. That's typically /usr/local/cuda or something similar.

Note that the cudatoolkit package installed by conda isn't really the full toolkit. It just contains the redistributable libraries needed at runtime. To compile programs that use CUDA, you need to get the full toolkit from NVIDIA.

virtualmartire commented 4 months ago

Hello,

Setting CMAKE_BUILD_TYPE=Release works for us (we are building without CUDA). "Configure" seems to works too, except this warning appears:

No project() command is present.  The top-level CMakeLists.txt file must
   contain a literal, direct call to the project() command.  Add a line of
   code such as

     project(ProjectName)

   near the top of the file, but after cmake_minimum_required().

   CMake is pretending there is a "project(Project)" command on the first
   line.

Also, "Generate" runs incredibly fast.

By the way, the installation doesn't end properly. On Mac we have this error:

[  4%] Building CXX object CMakeFiles/OpenMMNN.dir/openmmapi/src/NeuralNetworkForce.cpp.o
clang: warning: argument unused during compilation: '-msse2' [-Wunused-command-line-argument]
In file included from /Users/lucio/code/openmm-tensorflow/openmmapi/src/NeuralNetworkForce.cpp:32:
/Users/lucio/code/openmm-tensorflow/openmmapi/include/NeuralNetworkForce.h:35:10: fatal error: 'openmm/Context.h' file not found
#include "openmm/Context.h"
         ^~~~~~~~~~~~~~~~~~
1 error generated.
make[2]: *** [CMakeFiles/OpenMMNN.dir/openmmapi/src/NeuralNetworkForce.cpp.o] Error 1
make[1]: *** [CMakeFiles/OpenMMNN.dir/all] Error 2
make: *** [all] Error 2

while on Linux this one

[  7%] Building CXX object CMakeFiles/OpenMMNN.dir/openmmapi/src/NeuralNetworkForce.cpp.o
In file included from /root/test/openmm-tensorflow/openmmapi/src/NeuralNetworkForce.cpp:33:
/root/test/openmm-tensorflow/openmmapi/include/internal/NeuralNetworkForceImpl.h:38:10: fatal error: c_api.h: No such file or directory
   38 | #include <c_api.h>
      |          ^~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/OpenMMNN.dir/build.make:76: CMakeFiles/OpenMMNN.dir/openmmapi/src/NeuralNetworkForce.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:137: CMakeFiles/OpenMMNN.dir/all] Error 2
make: *** [Makefile:146: all] Error 2

What is happening? Thank you!

Appendix

I also append the cmake files below for completeness.

CMakeCache.txt (Linux)

# This is the CMakeCache file.
# For build in directory: /root/test/openmm-tensorflow/build
# It was generated by CMake: /usr/bin/cmake
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!.
# VALUE is the current value for the KEY.

########################
# EXTERNAL cache entries
########################

//Path to a program.
CMAKE_ADDR2LINE:FILEPATH=/usr/bin/addr2line

//Path to a program.
CMAKE_AR:FILEPATH=/usr/bin/ar

//Choose the type of build.  Options include: empty, Debug, Release,
// RelWithDebInfo, MinSizeRel.
CMAKE_BUILD_TYPE:STRING=Release

//Enable/Disable color output during build.
CMAKE_COLOR_MAKEFILE:BOOL=ON

//CXX compiler
CMAKE_CXX_COMPILER:FILEPATH=/usr/bin/c++

//A wrapper around 'ar' adding the appropriate '--plugin' option
// for the GCC compiler
CMAKE_CXX_COMPILER_AR:FILEPATH=/usr/bin/gcc-ar-12

//A wrapper around 'ranlib' adding the appropriate '--plugin' option
// for the GCC compiler
CMAKE_CXX_COMPILER_RANLIB:FILEPATH=/usr/bin/gcc-ranlib-12

//Flags used by the CXX compiler during all build types.
CMAKE_CXX_FLAGS:STRING=

//Flags used by the CXX compiler during DEBUG builds.
CMAKE_CXX_FLAGS_DEBUG:STRING=-g

//Flags used by the CXX compiler during MINSIZEREL builds.
CMAKE_CXX_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG

//Flags used by the CXX compiler during RELEASE builds.
CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG

//Flags used by the CXX compiler during RELWITHDEBINFO builds.
CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG

//C compiler
CMAKE_C_COMPILER:FILEPATH=/usr/bin/cc

//A wrapper around 'ar' adding the appropriate '--plugin' option
// for the GCC compiler
CMAKE_C_COMPILER_AR:FILEPATH=/usr/bin/gcc-ar-12

//A wrapper around 'ranlib' adding the appropriate '--plugin' option
// for the GCC compiler
CMAKE_C_COMPILER_RANLIB:FILEPATH=/usr/bin/gcc-ranlib-12

//Flags used by the C compiler during all build types.
CMAKE_C_FLAGS:STRING=

//Flags used by the C compiler during DEBUG builds.
CMAKE_C_FLAGS_DEBUG:STRING=-g

//Flags used by the C compiler during MINSIZEREL builds.
CMAKE_C_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG

//Flags used by the C compiler during RELEASE builds.
CMAKE_C_FLAGS_RELEASE:STRING=-O3 -DNDEBUG

//Flags used by the C compiler during RELWITHDEBINFO builds.
CMAKE_C_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG

//Path to a program.
CMAKE_DLLTOOL:FILEPATH=CMAKE_DLLTOOL-NOTFOUND

//Flags used by the linker during all build types.
CMAKE_EXE_LINKER_FLAGS:STRING=

//Flags used by the linker during DEBUG builds.
CMAKE_EXE_LINKER_FLAGS_DEBUG:STRING=

//Flags used by the linker during MINSIZEREL builds.
CMAKE_EXE_LINKER_FLAGS_MINSIZEREL:STRING=

//Flags used by the linker during RELEASE builds.
CMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=

//Flags used by the linker during RELWITHDEBINFO builds.
CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO:STRING=

//Enable/Disable output of compile commands during generation.
CMAKE_EXPORT_COMPILE_COMMANDS:BOOL=

//Value Computed by CMake.
CMAKE_FIND_PACKAGE_REDIRECTS_DIR:STATIC=/root/test/openmm-tensorflow/build/CMakeFiles/pkgRedirects

//Where to install the plugin
CMAKE_INSTALL_PREFIX:PATH=/usr/local/openmm

//Path to a program.
CMAKE_LINKER:FILEPATH=/usr/bin/ld

//Path to a program.
CMAKE_MAKE_PROGRAM:FILEPATH=/usr/bin/gmake

//Flags used by the linker during the creation of modules during
// all build types.
CMAKE_MODULE_LINKER_FLAGS:STRING=

//Flags used by the linker during the creation of modules during
// DEBUG builds.
CMAKE_MODULE_LINKER_FLAGS_DEBUG:STRING=

//Flags used by the linker during the creation of modules during
// MINSIZEREL builds.
CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL:STRING=

//Flags used by the linker during the creation of modules during
// RELEASE builds.
CMAKE_MODULE_LINKER_FLAGS_RELEASE:STRING=

Luciano Colosio, [15/04/24 17:58]
//Flags used by the linker during the creation of modules during
// RELWITHDEBINFO builds.
CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING=

//Path to a program.
CMAKE_NM:FILEPATH=/usr/bin/nm

//Path to a program.
CMAKE_OBJCOPY:FILEPATH=/usr/bin/objcopy

//Path to a program.
CMAKE_OBJDUMP:FILEPATH=/usr/bin/objdump

//Value Computed by CMake
CMAKE_PROJECT_DESCRIPTION:STATIC=

//Value Computed by CMake
CMAKE_PROJECT_HOMEPAGE_URL:STATIC=

//Value Computed by CMake
CMAKE_PROJECT_NAME:STATIC=Project

//Path to a program.
CMAKE_RANLIB:FILEPATH=/usr/bin/ranlib

//Path to a program.
CMAKE_READELF:FILEPATH=/usr/bin/readelf

//Flags used by the linker during the creation of shared libraries
// during all build types.
CMAKE_SHARED_LINKER_FLAGS:STRING=

//Flags used by the linker during the creation of shared libraries
// during DEBUG builds.
CMAKE_SHARED_LINKER_FLAGS_DEBUG:STRING=

//Flags used by the linker during the creation of shared libraries
// during MINSIZEREL builds.
CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL:STRING=

//Flags used by the linker during the creation of shared libraries
// during RELEASE builds.
CMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING=

//Flags used by the linker during the creation of shared libraries
// during RELWITHDEBINFO builds.
CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO:STRING=

//If set, runtime paths are not added when installing shared libraries,
// but are added when building.
CMAKE_SKIP_INSTALL_RPATH:BOOL=NO

//If set, runtime paths are not added when using shared libraries.
CMAKE_SKIP_RPATH:BOOL=NO

//Flags used by the linker during the creation of static libraries
// during all build types.
CMAKE_STATIC_LINKER_FLAGS:STRING=

//Flags used by the linker during the creation of static libraries
// during DEBUG builds.
CMAKE_STATIC_LINKER_FLAGS_DEBUG:STRING=

//Flags used by the linker during the creation of static libraries
// during MINSIZEREL builds.
CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL:STRING=

//Flags used by the linker during the creation of static libraries
// during RELEASE builds.
CMAKE_STATIC_LINKER_FLAGS_RELEASE:STRING=

//Flags used by the linker during the creation of static libraries
// during RELWITHDEBINFO builds.
CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING=

//Path to a program.
CMAKE_STRIP:FILEPATH=/usr/bin/strip

//If this value is on, makefiles will be generated without the
// .SILENT directive, and all commands will be echoed to the console
// during the make.  This is useful for debugging only. With Visual
// Studio IDE projects all commands are done without /nologo.
CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE

//Compile device code in 64 bit mode
CUDA_64_BIT_DEVICE_CODE:BOOL=ON

//Attach the build rule to the CUDA source file.  Enable only when
// the CUDA source file is added to at most one target.
CUDA_ATTACH_VS_BUILD_RULE_TO_CUDA_FILE:BOOL=ON

//Generate and parse .cubin files in Device mode.
CUDA_BUILD_CUBIN:BOOL=OFF

//Build in Emulation mode
CUDA_BUILD_EMULATION:BOOL=OFF

//"cudart" library
CUDA_CUDART_LIBRARY:FILEPATH=CUDA_CUDART_LIBRARY-NOTFOUND

//"cuda" library (older versions only).
CUDA_CUDA_LIBRARY:FILEPATH=CUDA_CUDA_LIBRARY-NOTFOUND

//Directory to put all the output files.  If blank it will default
// to the CMAKE_CURRENT_BINARY_DIR
CUDA_GENERATED_OUTPUT_DIR:PATH=

//Generated file extension
CUDA_HOST_COMPILATION_CPP:BOOL=ON

//Host side compiler used by NVCC
CUDA_HOST_COMPILER:FILEPATH=/usr/bin/cc

//Path to a program.
CUDA_NVCC_EXECUTABLE:FILEPATH=CUDA_NVCC_EXECUTABLE-NOTFOUND

//Semi-colon delimit multiple arguments. during all build types.
CUDA_NVCC_FLAGS:STRING=

//Semi-colon delimit multiple arguments. during DEBUG builds.
CUDA_NVCC_FLAGS_DEBUG:STRING=

//Semi-colon delimit multiple arguments. during MINSIZEREL builds.
CUDA_NVCC_FLAGS_MINSIZEREL:STRING=

//Semi-colon delimit multiple arguments. during RELEASE builds.
CUDA_NVCC_FLAGS_RELEASE:STRING=

//Semi-colon delimit multiple arguments. during RELWITHDEBINFO
// builds.
CUDA_NVCC_FLAGS_RELWITHDEBINFO:STRING=

//Propagate C/CXX_FLAGS and friends to the host compiler via -Xcompile
CUDA_PROPAGATE_HOST_FLAGS:BOOL=ON

Luciano Colosio, [15/04/24 17:58]
//Path to a file.
CUDA_SDK_ROOT_DIR:PATH=CUDA_SDK_ROOT_DIR-NOTFOUND

//Compile CUDA objects with separable compilation enabled.  Requires
// CUDA 5.0+
CUDA_SEPARABLE_COMPILATION:BOOL=OFF

//Path to a file.
CUDA_TOOLKIT_INCLUDE:PATH=CUDA_TOOLKIT_INCLUDE-NOTFOUND

//Print out the commands run while compiling the CUDA source file.
//  With the Makefile generator this defaults to VERBOSE variable
// specified on the command line, but can be forced on with this
// option.
CUDA_VERBOSE_BUILD:BOOL=OFF

//"cublas" library
CUDA_cublas_LIBRARY:FILEPATH=CUDA_cublas_LIBRARY-NOTFOUND

//"cublasemu" library
CUDA_cublasemu_LIBRARY:FILEPATH=CUDA_cublasemu_LIBRARY-NOTFOUND

//"cufft" library
CUDA_cufft_LIBRARY:FILEPATH=CUDA_cufft_LIBRARY-NOTFOUND

//"cufftemu" library
CUDA_cufftemu_LIBRARY:FILEPATH=CUDA_cufftemu_LIBRARY-NOTFOUND

//Build implementation for CUDA
NN_BUILD_CUDA_LIB:BOOL=OFF

//Build implementation for OpenCL
NN_BUILD_OPENCL_LIB:BOOL=OFF

//Build wrappers for Python
NN_BUILD_PYTHON_WRAPPERS:BOOL=ON

//Path to a file.
OPENCL_INCLUDE_DIR:PATH=OPENCL_INCLUDE_DIR-NOTFOUND

//Path to a library.
OPENCL_LIBRARY:FILEPATH=OPENCL_LIBRARY-NOTFOUND

//Where OpenMM is installed
OPENMM_DIR:PATH=/usr/local/openmm

//Dependencies for the target
OpenMMNNReference_LIB_DEPENDS:STATIC=general;OpenMM;debug;OpenMMNN;optimized;OpenMMNN;

//Dependencies for the target
OpenMMNN_LIB_DEPENDS:STATIC=general;OpenMM;general;tensorflow;

//Path to a program.
PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python

//Value Computed by CMake
Project_BINARY_DIR:STATIC=/root/test/openmm-tensorflow/build

//Value Computed by CMake
Project_IS_TOP_LEVEL:STATIC=ON

//Value Computed by CMake
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unlucio commented 4 months ago

I'm having the same problem, stuck at build with those errors (might be the old age but I feel ./configure && make && make install were better at reporting errors than ccmake's UI)

peastman commented 4 months ago

That probably means you have OPENMM_DIR set incorrectly. It should point to the base of your OpenMM installation. Inside that directory, there should be another directory called include which contains another directory called openmm.

unlucio commented 4 months ago

I tried cloning openmm pointing OPENMM_DIR to the repo's dir but ccmakeenv's screen was still showing OPENMM_DIR=/usr/local/openmm, so I compiled openmm which got correctly installed to /usr/local/openmm:

but when I try to compile

thalia openmm-tensorflow (master?) # make
[  7%] Building CXX object CMakeFiles/OpenMMNN.dir/openmmapi/src/NeuralNetworkForce.cpp.o
In file included from /root/test/openmm-tensorflow/openmmapi/src/NeuralNetworkForce.cpp:33:
/root/test/openmm-tensorflow/openmmapi/include/internal/NeuralNetworkForceImpl.h:38:10: fatal error: c_api.h: No such file or directory
   38 | #include <c_api.h>
      |          ^~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/OpenMMNN.dir/build.make:76: CMakeFiles/OpenMMNN.dir/openmmapi/src/NeuralNetworkForce.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:137: CMakeFiles/OpenMMNN.dir/all] Error 2
make: *** [Makefile:146: all] Error 2

thalia is an Ubuntu 22.10 running:

make -version
GNU Make 4.3
Built for x86_64-pc-linux-gnu
Copyright (C) 1988-2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

cmake --version
cmake version 3.24.2

CMake suite maintained and supported by Kitware (kitware.com/cmake).

ldd --version
ldd (Ubuntu GLIBC 2.36-0ubuntu4) 2.36
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

 gcc --version
gcc (Ubuntu 12.2.0-3ubuntu1) 12.2.0
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Since the repo's code is so old - I don't mean it in a negative way, "if it ain't broken don't fix it", tho toolings and environments around it might have changed meanwhile - can you share infos on an environment that is sure to be able to compile this library?

peastman commented 4 months ago

I tried cloning openmm pointing OPENMM_DIR to the repo's dir

It needs to point to the installed package, not the source code repo.

I haven't done anything with TensorFlow in years. The field has mostly standardized on PyTorch, so that's where all our current development work is focused. See https://github.com/openmm/openmm-torch. If current versions of TensorFlow require changes to compile, a PR with the changes would be welcome.

unlucio commented 4 months ago

As said in the prev post openmm was compiled and installed in /usr/local/openmm, since simply compiling it in place and pointing OPENMM_DIR to wasn't pick up by ccmake who would still display OPENMM_DIR=/usr/local/openmm. You can see in the screenshot I posted that /usr/local/openmm looks coherent with your suggestions, yet compilation still booms on me with:

thalia openmm-tensorflow (master?) # make
[  7%] Building CXX object CMakeFiles/OpenMMNN.dir/openmmapi/src/NeuralNetworkForce.cpp.o
In file included from /root/test/openmm-tensorflow/openmmapi/src/NeuralNetworkForce.cpp:33:
/root/test/openmm-tensorflow/openmmapi/include/internal/NeuralNetworkForceImpl.h:38:10: fatal error: c_api.h: No such file or directory
   38 | #include <c_api.h>
      |          ^~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/OpenMMNN.dir/build.make:76: CMakeFiles/OpenMMNN.dir/openmmapi/src/NeuralNetworkForce.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:137: CMakeFiles/OpenMMNN.dir/all] Error 2
make: *** [Makefile:146: all] Error 2

I'll be more than happy to send over some good Docker PR, so nobody else will need to deal with compilation dependencies like it was the 90s 😆, once I figure out how to compile it 😅. That was the intrinsic direction asking about an environment that can compile it, so I can reproduce it with Docker.

peastman commented 4 months ago

c_api.h contains the TensorFlow C API. It gets located based on TENSORFLOW_DIR:

https://github.com/openmm/openmm-tensorflow/blob/c9a0e09cdb2c9449fca5cf02fe9e000c4757a721/CMakeLists.txt#L14

You have it set to /usr/local. Since you installed it with conda, that's probably not the correct location.

openmm / openmm-tensorflow

CMAKE_BUILD_TYPE and CUDA_SDK_ROOT_DIR #18

Appendix

CMakeCache.txt (Linux)

CMakeCache.txt (Mac)

cmake_install.cmake (Mac)

Makefile (Mac)