Open jamesdalg opened 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 |
+---------------------------------------------------------------------------------------+
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.
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!
I also append the cmake files below for completeness.
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Luciano Colosio, [15/04/24 17:58]
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Luciano Colosio, [15/04/24 17:58]
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Luciano Colosio, [15/04/24 17:58]
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.PHONY : help
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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)
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
.
I tried cloning openmm pointing OPENMM_DIR
to the repo's dir but ccmake
env'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?
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.
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.
c_api.h
contains the TensorFlow C API. It gets located based on TENSORFLOW_DIR
:
You have it set to /usr/local
. Since you installed it with conda, that's probably not the correct location.
I am attempting to install openmm-tensorflow and am getting a prompt in ccmake about the build type and the CUDA_SDK_ROOT_DIR.
I have configured my environment as the following:
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.