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Errors when running `make test`
Thank you for creating this plugin!
I am having an issue during the installation process. I am able to successfully run the make and make install commands. However, when I run make test, all of the tests fail, as shown below.
Running tests...
/common/software/install/spack/linux-centos7-ivybridge/gcc-13.1.0/cmake-3.26.3-em4tlmoxf4uhny57w2i5f6vfdfk6v4wy/bin/ctest --force-new-ctest-process
Test project gopal145/software/openmm_deepmd_plugin/build
Start 1: TestSerializeDeepmdForce
1/5 Test #1: TestSerializeDeepmdForce .........***Failed 3.20 sec
Start 2: TestDeepmdPlugin4Reference
2/5 Test #2: TestDeepmdPlugin4Reference .......***Failed 0.58 sec
Start 3: TestDeepmdPlugin4CUDASingle
3/5 Test #3: TestDeepmdPlugin4CUDASingle ......Subprocess aborted***Exception: 0.77 sec
Start 4: TestDeepmdPlugin4CUDAMixed
4/5 Test #4: TestDeepmdPlugin4CUDAMixed .......Subprocess aborted***Exception: 0.60 sec
Start 5: TestDeepmdPlugin4CUDADouble
5/5 Test #5: TestDeepmdPlugin4CUDADouble ......Subprocess aborted***Exception: 0.60 sec
0% tests passed, 5 tests failed out of 5
Total Test time (real) = 5.78 sec
The following tests FAILED:
1 - TestSerializeDeepmdForce (Failed)
2 - TestDeepmdPlugin4Reference (Failed)
3 - TestDeepmdPlugin4CUDASingle (Subprocess aborted)
4 - TestDeepmdPlugin4CUDAMixed (Subprocess aborted)
5 - TestDeepmdPlugin4CUDADouble (Subprocess aborted)
Errors while running CTest
I looked at the test log file located at build/Testing/Temporary/LastTest.log and I see the following message:
Start testing: Dec 06 20:00 CST
----------------------------------------------------------
1/5 Testing: TestSerializeDeepmdForce
1/5 Test: TestSerializeDeepmdForce
Command: "gopal145/software/openmm_deepmd_plugin/build/TestSerializeDeepmdForce"
Directory: gopal145/software/openmm_deepmd_plugin/build
"TestSerializeDeepmdForce" start time: Dec 06 20:00 CST
Output:
----------------------------------------------------------
DeePMD-kit: Successfully load libcudart.so
DeePMD-kit WARNING: Environmental variable TF_INTRA_OP_PARALLELISM_THREADS is not set. Tune TF_INTRA_OP_PARALLELISM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DeePMD-kit WARNING: Environmental variable TF_INTER_OP_PARALLELISM_THREADS is not set. Tune TF_INTER_OP_PARALLELISM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DeePMD-kit WARNING: Environmental variable OMP_NUM_THREADS is not set. Tune OMP_NUM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DATA_LOSS: Can't parse ../python/OpenMMDeepmdPlugin/data/water.pb as binary proto
exception: DeePMD-kit C API Error: DeePMD-kit Error: TensorFlow Error: DATA_LOSS: Can't parse ../python/OpenMMDeepmdPlugin/data/water.pb as binary proto
<end of output>
Test time = 3.20 sec
----------------------------------------------------------
Test Failed.
"TestSerializeDeepmdForce" end time: Dec 06 20:00 CST
"TestSerializeDeepmdForce" time elapsed: 00:00:03
----------------------------------------------------------
The remaining 4 tests all fail for a similar reason. I have verified that the water.pb file does exist. I understand that the warning states that certain environment variables are not set, but I am not sure it would cause the following error. I also looked at issue #9 and exported the LD_LIBRARY_PATH variable, but I observed the same error. Can someone please provide some assistance? Thank you.
strange boxes when using the qdpi model
Thanks for this nice module!
I am trying to use the QDpi Model, for running a MD simulation describing the whole waterbox with the NNP, following this comment
Alternatively, are you specifically interested in running a simulation solely using the trained NNP model?
If you want a simulation with NNP only, the Deepmd Plugin is enough to use.
If I run the NVT test script provided within this repository (https://github.com/JingHuangLab/openmm_deepmd_plugin/blob/master/python/tests/test_deepmd_nvt.py) I can run this test with the provided water.pb file and everything looks nice. If I now change the water.pb to the qdpi model (qdpi-1.0.pb), the waterbox is exploding:
#"Progress (%)" "Step" "Time (ps)" "Potential Energy (kJ/mole)" "Kinetic Energy (kJ/mole)" "Total Energy (kJ/mole)" "Temperature (K)" "Density (g/mL)" "Speed (ns/day)" "Time Remaining"
10.0% 100 0.01999999999999999 -48617782.74773688 5991.949569741136 -48611790.79816714 625.5780260850828 0.9854098249994789 0 --
20.0% 200 0.03999999999999987 -48619461.151101604 8961.926531253604 -48610499.22457035 935.6527861404164 0.9854098249994789 0.243 0:56
30.0% 300 0.05999999999999975 -48621288.31182224 18550.951134558753 -48602737.36068769 1936.776546211729 0.9854098249994789 0.233 0:52
40.0% 400 0.08000000000000024 -48622517.24254719 24885.054267470026 -48597632.18827972 2598.0764601689757 0.9854098249994789 0.231 0:44
Am I doing something wrong or is this a problem of the used NNP model?
Eoorr: Error loading CUDA module
Thanks for this nice module!
I am trying to use the openmm with dp model for running a MD simulation, Some CUDA errors occur. My test GPU models were 3090 and V100. nvidia-driver-525. The following is a detailed description of the error. How to solve this kind of error?
#######################################################################################
DeePMD-kit: Successfully load libcudart.so
Matplotlib created a temporary cache directory at /tmp/matplotlib-qhzu1vhe because the default path (/HOME/scz0btj/.cache/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
DeePMD-kit WARNING: Environmental variable TF_INTRA_OP_PARALLELISM_THREADS is not set. Tune TF_INTRA_OP_PARALLELISM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DeePMD-kit WARNING: Environmental variable TF_INTER_OP_PARALLELISM_THREADS is not set. Tune TF_INTER_OP_PARALLELISM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
DeePMD-kit WARNING: Environmental variable OMP_NUM_THREADS is not set. Tune OMP_NUM_THREADS for the best performance. See https://deepmd.rtfd.io/parallelism/ for more information.
2023-11-25 22:17:09.632661: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
Traceback (most recent call last):
File "/input_lbg-12767-9901414/run_nvt.py", line 66, in
simulation = Simulation(pdb.topology, dp_system, integrator, platform, properties)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/dp_omm/lib/python3.11/site-packages/openmm/app/simulation.py", line 103, in init
self.context = mm.Context(self.system, self.integrator, platform, platformProperties)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/dp_omm/lib/python3.11/site-packages/openmm/openmm.py", line 3749, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222)
Installation failed
I have followed your Installation guidance in READMD.md.
However, I encounter some difficulties in the Installation process.
My OPENMM_INSTALLED_DIR is the env direction of anaconda which installed the openmm by conda (/home/xuzp/WORK/shipengjie/01-app/anaconda/envs/dp_openmm)
My LIBDEEPMD_C_INSTALLED_DIR is the direction of C++ API download by wget
(/home/xuzp/WORK/shipengjie/01-app/openmm_dp/libdeepmd_c_2.2.1)
When I execute “cmake”, the log information is:
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to: /home/xuzp/WORK/shipengjie/01-app/openmm_dp/openmm_deepmd_plugin/build
It looks fine. Then I execute make:
[ 5%] Building CXX object CMakeFiles/OpenMMDeepmd.dir/openmmapi/src/DeepmdForce.cpp.o
[ 10%] Building CXX object CMakeFiles/OpenMMDeepmd.dir/openmmapi/src/DeepmdForceImpl.cpp.o
[ 15%] Building CXX object CMakeFiles/OpenMMDeepmd.dir/serialization/src/DeepmdForceProxy.cpp.o
[ 21%] Building CXX object CMakeFiles/OpenMMDeepmd.dir/serialization/src/DeepmdSerializationProxyRegistration.cpp.o
[ 26%] Linking CXX shared library libOpenMMDeepmd.so
[ 26%] Built target OpenMMDeepmd
[ 31%] Building CXX object serialization/tests/CMakeFiles/TestSerializeDeepmdForce.dir/TestSerializeDeepmdForce.cpp.o
[ 36%] Linking CXX executable ../../TestSerializeDeepmdForce
CMakeFiles/TestSerializeDeepmdForce.dir/TestSerializeDeepmdForce.cpp.o：在函数‘testSerialization()’中：
TestSerializeDeepmdForce.cpp:(.text+0x3f7)：对‘OpenMM::throwException(char const*, int, std::string const&)’未定义的引用
CMakeFiles/TestSerializeDeepmdForce.dir/TestSerializeDeepmdForce.cpp.o：在函数‘void OpenMM::XmlSerializer::serialize<DeepmdPlugin::DeepmdForce>(DeepmdPlugin::DeepmdForce const*, std::string const&, std::ostream&)’中：
TestSerializeDeepmdForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN12DeepmdPlugin11DeepmdForceEEEvPKT_RKSsRSo[_ZN6OpenMM13XmlSerializer9serializeIN12DeepmdPlugin11DeepmdForceEEEvPKT_RKSsRSo]+0x6b)：对‘OpenMM::SerializationNode::setName(std::string const&)’未定义的引用
TestSerializeDeepmdForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN12DeepmdPlugin11DeepmdForceEEEvPKT_RKSsRSo[_ZN6OpenMM13XmlSerializer9serializeIN12DeepmdPlugin11DeepmdForceEEEvPKT_RKSsRSo]+0xce)：对‘OpenMM::SerializationNode::hasProperty(std::string const&) const’未定义的引用
TestSerializeDeepmdForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN12DeepmdPlugin11DeepmdForceEEEvPKT_RKSsRSo[_ZN6OpenMM13XmlSerializer9serializeIN12DeepmdPlugin11DeepmdForceEEEvPKT_RKSsRSo]+0x105)：对‘OpenMM::SerializationProxy::getTypeName() const’未定义的引用
TestSerializeDeepmdForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN12DeepmdPlugin11DeepmdForceEEEvPKT_RKSsRSo[_ZN6OpenMM13XmlSerializer9serializeIN12DeepmdPlugin11DeepmdForceEEEvPKT_RKSsRSo]+0x155)：对‘OpenMM::SerializationProxy::getTypeName() const’未定义的引用
TestSerializeDeepmdForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN12DeepmdPlugin11DeepmdForceEEEvPKT_RKSsRSo[_ZN6OpenMM13XmlSerializer9serializeIN12DeepmdPlugin11DeepmdForceEEEvPKT_RKSsRSo]+0x192)：对‘OpenMM::SerializationNode::setStringProperty(std::string const&, std::string const&)’未定义的引用
../../libOpenMMDeepmd.so：对‘OpenMM::SerializationProxy::SerializationProxy(std::string const&)’未定义的引用
../../libOpenMMDeepmd.so：对‘OpenMM::Platform::createKernel(std::string const&, OpenMM::ContextImpl&) const’未定义的引用
../../libOpenMMDeepmd.so：对‘OpenMM::SerializationNode::setIntProperty(std::string const&, int)’未定义的引用
../../libOpenMMDeepmd.so：对‘OpenMM::SerializationNode::getIntProperty(std::string const&) const’未定义的引用
../../libOpenMMDeepmd.so：对‘OpenMM::SerializationNode::getStringProperty(std::string const&) const’未定义的引用
collect2: 错误：ld 返回 1
make[2]: *** [TestSerializeDeepmdForce] 错误 1
make[1]: *** [serialization/tests/CMakeFiles/TestSerializeDeepmdForce.dir/all] 错误 2
make: *** [all] 错误 2
(dp_openmm) [xuzp@c13b02n04 build]$ echo ${LIBDEEPMD_C_INSTALLED_DIR}
/home/xuzp/WORK/shipengjie/01-app/openmm_dp/libdeepmd_c_2.2.1
(dp_openmm) [xuzp@c13b02n04 build]$ echo ${OPENMM_INSTALLED_DIR}
/home/xuzp/WORK/shipengjie/01-app/anaconda/envs/dp_openmm
It has undefined reference error.
I don't know where the problem is.
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