undefined::reference error during building from source

[ndonyapour]

Hello,
I’m trying to build Opemm-torch from source, and I get an undefined reference error. This error happens when I install Pytroch from PyTorch channel via Conda. I believe this error relates to the compiling of OpenMM with the old C++ ABI. I tried installing OpenMM from source with the new C++11 AB, but still, I got the same error.

Environment config:

• OpenMM7.7.0 from condaforge
• PyTorch 1.10.2 from pytoch
• GNU 8.5.0

Commands for compiling Opemm-torch

export Torch_DIR="$(python -c 'import torch.utils; print(torch.utils.cmake_prefix_path)')"
cmake  ..
ccmake -i ..
make install

Error:

[ 36%] Linking CXX executable ../../TestSerializeTorchForce
CMakeFiles/TestSerializeTorchForce.dir/TestSerializeTorchForce.cpp.o: In function `testSerialization()':
TestSerializeTorchForce.cpp:(.text+0x35a): undefined reference to `OpenMM::throwException(char const*, int, std::string const&)'
TestSerializeTorchForce.cpp:(.text+0x447): undefined reference to `OpenMM::throwException(char const*, int, std::string const&)'
TestSerializeTorchForce.cpp:(.text+0x534): undefined reference to `OpenMM::throwException(char const*, int, std::string const&)'
TestSerializeTorchForce.cpp:(.text+0x665): undefined reference to `OpenMM::throwException(char const*, int, std::string const&)'
TestSerializeTorchForce.cpp:(.text+0x77e): undefined reference to `OpenMM::throwException(char const*, int, std::string const&)'
CMakeFiles/TestSerializeTorchForce.dir/TestSerializeTorchForce.cpp.o:TestSerializeTorchForce.cpp:(.text+0x890): more undefined references to `OpenMM::throwException(char const*, int, std::string const&)' follow
CMakeFiles/TestSerializeTorchForce.dir/TestSerializeTorchForce.cpp.o: In function `void OpenMM::XmlSerializer::serialize<TorchPlugin::TorchForce>(TorchPlugin::TorchForce const*, std::string const&, std::ostream&)':
TestSerializeTorchForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN11TorchPlugin10TorchForceEEEvPKT_RKSsRSo[_ZN6OpenMM13XmlSerializer9serializeIN11TorchPlugin10TorchForceEEEvPKT_RKSsRSo]+0x66): undefined reference to `OpenMM::SerializationNode::setName(std::string const&)'
TestSerializeTorchForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN11TorchPlugin10TorchForceEEEvPKT_RKSsRSo[_ZN6OpenMM13XmlSerializer9serializeIN11TorchPlugin10TorchForceEEEvPKT_RKSsRSo]+0xc9): undefined reference to `OpenMM::SerializationNode::hasProperty(std::string const&) const'
TestSerializeTorchForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN11TorchPlugin10TorchForceEEEvPKT_RKSsRSo[_ZN6OpenMM13XmlSerializer9serializeIN11TorchPlugin10TorchForceEEEvPKT_RKSsRSo]+0x100): undefined reference to `OpenMM::SerializationProxy::getTypeName() const'
TestSerializeTorchForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN11TorchPlugin10TorchForceEEEvPKT_RKSsRSo[_ZN6OpenMM13XmlSerializer9serializeIN11TorchPlugin10TorchForceEEEvPKT_RKSsRSo]+0x150): undefined reference to `OpenMM::SerializationProxy::getTypeName() const'
TestSerializeTorchForce.cpp:(.text._ZN6OpenMM13XmlSerializer9serializeIN11TorchPlugin10TorchForceEEEvPKT_RKSsRSo[_ZN6OpenMM13XmlSerializer9serializeIN11TorchPlugin10TorchForceEEEvPKT_RKSsRSo]+0x18d): undefined reference to `OpenMM::SerializationNode::setStringProperty(std::string const&, std::string const&)'
../../libOpenMMTorch.so: undefined reference to `OpenMM::Platform::createKernel(std::string const&, OpenMM::ContextImpl&) const'
../../libOpenMMTorch.so: undefined reference to `OpenMM::SerializationNode::setBoolProperty(std::string const&, bool)'
../../libOpenMMTorch.so: undefined reference to `OpenMM::SerializationNode::getDoubleProperty(std::string const&) const'
../../libOpenMMTorch.so: undefined reference to `OpenMM::SerializationNode::setIntProperty(std::string const&, int)'
../../libOpenMMTorch.so: undefined reference to `OpenMM::SerializationNode::getIntProperty(std::string const&) const'
../../libOpenMMTorch.so: undefined reference to `OpenMM::SerializationProxy::SerializationProxy(std::string const&)'
../../libOpenMMTorch.so: undefined reference to `OpenMM::SerializationNode::getBoolProperty(std::string const&) const'
../../libOpenMMTorch.so: undefined reference to `OpenMM::SerializationNode::getStringProperty(std::string const&) const'
../../libOpenMMTorch.so: undefined reference to `OpenMM::SerializationNode::getName() const'
../../libOpenMMTorch.so: undefined reference to `OpenMM::SerializationNode::createChildNode(std::string const&)'
../../libOpenMMTorch.so: undefined reference to `OpenMM::SerializationNode::setDoubleProperty(std::string const&, double)'
../../libOpenMMTorch.so: undefined reference to `OpenMM::SerializationNode::getIntProperty(std::string const&, int) const'
collect2: error: ld returned 1 exit status
make[2]: *** [serialization/tests/CMakeFiles/TestSerializeTorchForce.dir/build.make:117: TestSerializeTorchForce] Error 1
make[1]: *** [CMakeFiles/Makefile2:315: serialization/tests/CMakeFiles/TestSerializeTorchForce.dir/all] Error 2
make: *** [Makefile:160: all] Error 2

Any idea?

Thank you.

[raimis]

OpenMM, like any other package on conda-forge, are built with the new C++11 ABI. The packages from the PyTorch channel are build with the old C++ ABI, so they aren't compatible.

From the error message, I can see that you are building with the old C++ ABI, so I won't link with OpenMM from conda-forge.

[ndonyapour]

Thank you, this solved my problem. It seems that I've been compiling OpenMM with the new C++11 ABI and setting the CMAKE_FLAGS+=" -D_GLIBCXX_USE_CXX11_ABI=0" flag during compiling fixed the issue.
I just wanted to see if I installed all packages from conda-forge would work because all packages are compiled with the same version of ABI. However, I got the undefined reference linking error again.

Error:

/home/user/anaconda3/envs/foregpkgs/lib/python3.9/site-packages/torch/lib/libtorch_cpu.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream()@GLIBCXX_3.4.26'
/home/user/anaconda3/pkgs/openmm-7.7.0-py39h792354b_0/lib/libOpenMM.so: undefined reference to `std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::basic_stringstream()@GLIBCXX_3.4.26'
collect2: error: ld returned 1 exit status
make[2]: *** [serialization/tests/CMakeFiles/TestSerializeTorchForce.dir/build.make:118: TestSerializeTorchForce] Error 1
make[1]: *** [CMakeFiles/Makefile2:315: serialization/tests/CMakeFiles/TestSerializeTorchForce.dir/all] Error 2
make: *** [Makefile:160: all] Error 2

[ndonyapour]

I hit another error while importing OpenMM (installed from source using -D_GLIBCXX_USE_CXX11_ABI=0). Here is the error, and I can't figure out how to fix it.

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/user/anaconda3/envs/fltop/lib/python3.9/site-packages/openmm/__init__.py", line 19, in <module>
    from openmm.openmm import *
  File "/home/user/anaconda3/envs/fltop/lib/python3.9/site-packages/openmm/openmm.py", line 13, in <module>
    from . import _openmm
ImportError: /home/user/anaconda3/envs/fltop/lib/python3.9/site-packages/openmm/_openmm.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZN6OpenMM23CustomCentroidBondForce20addTabulatedFunctionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS_17TabulatedFunctionE

[ndonyapour]

I hit another error while importing OpenMM (installed from source using -D_GLIBCXX_USE_CXX11_ABI=0). Here is the error, and I can't figure out how to fix it.

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/user/anaconda3/envs/fltop/lib/python3.9/site-packages/openmm/__init__.py", line 19, in <module>
    from openmm.openmm import *
  File "/home/user/anaconda3/envs/fltop/lib/python3.9/site-packages/openmm/openmm.py", line 13, in <module>
    from . import _openmm
ImportError: /home/user/anaconda3/envs/fltop/lib/python3.9/site-packages/openmm/_openmm.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZN6OpenMM23CustomCentroidBondForce20addTabulatedFunctionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS_17TabulatedFunctionE

I fixed this issue by adding -D_GLIBCXX_USE_CXX11_ABI=0 to extra_compile_args in the setup.py file.

[ndonyapour]

I apologize for posting multiple messages here. Now, I get an error when I dopython -c "import openmmtorch". I think this one is also related to the C++11 ABI as well.

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/user/anaconda3/envs/fltop/lib/python3.9/site-packages/openmmtorch.py", line 15, in <module>
    import _openmmtorch
ImportError: /home/user/anaconda3/envs/fltop/lib/python3.9/site-packages/_openmmtorch.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZNK11TorchPlugin10TorchForce22getGlobalParameterNameB5cxx11Ei

[ndonyapour]

I apologize for posting multiple messages here. Now, I get an error when I dopython -c "import openmmtorch". I think this one is also related to the C++11 ABI as well.

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/user/anaconda3/envs/fltop/lib/python3.9/site-packages/openmmtorch.py", line 15, in <module>
    import _openmmtorch
ImportError: /home/user/anaconda3/envs/fltop/lib/python3.9/site-packages/_openmmtorch.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZNK11TorchPlugin10TorchForce22getGlobalParameterNameB5cxx11Ei

I was able to fix this issue by compiling the plugin code with -D_GLIBCXX_USE_CXX11_ABI=0 and adding this flag to its setup.py file. I was wondering if this is the right way to resolve this issue?

[raimis]

Provided you build all the components with the old C++ ABI, it should work.

[ndonyapour]

Thank you, this solved my problem. It seems that I've been compiling OpenMM with the new C++11 ABI and setting the CMAKE_FLAGS+=" -D_GLIBCXX_USE_CXX11_ABI=0" flag during compiling fixed the issue. I just wanted to see if I installed all packages from conda-forge would work because all packages are compiled with the same version of ABI. However, I got the undefined reference linking error again.

Error:

/home/user/anaconda3/envs/foregpkgs/lib/python3.9/site-packages/torch/lib/libtorch_cpu.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream()@GLIBCXX_3.4.26'
/home/user/anaconda3/pkgs/openmm-7.7.0-py39h792354b_0/lib/libOpenMM.so: undefined reference to `std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::basic_stringstream()@GLIBCXX_3.4.26'
collect2: error: ld returned 1 exit status
make[2]: *** [serialization/tests/CMakeFiles/TestSerializeTorchForce.dir/build.make:118: TestSerializeTorchForce] Error 1
make[1]: *** [CMakeFiles/Makefile2:315: serialization/tests/CMakeFiles/TestSerializeTorchForce.dir/all] Error 2
make: *** [Makefile:160: all] Error 2

Ok, thanks! Any suggestions about this one?

[raimis]

Looks your are linking OpenMM and PyTorch with the new C++ ABI; and the C++ runtime (libstdc++.so), which doesn't support the new C++ ABI.

[ndonyapour]

I have updated GNU from 8.5 to 11.2 and Cudatoolkit from 11.3 to 11.6 and still getting the linker error.

[ndonyapour]

I found two methods for fixing the linker errors coming from the C++11 ABI:

1- Install PyTorch from source which sets -D_GLIBCXX_USE_CXX11_ABI=1 and then get other packages from Conda-forge, finally you can build openmm-torch

2- Create a conda virtual environment from the yml file I uploaded here and follow the commands below for building and installing openmm-torch

conda env create -n optorchenv -f environment.yml
conda activate optorchenv 
git clone https://github.com/openmm/openmm-torch.git
cd openmm-torch
mkdir build && cd build
export Torch_DIR="$(python -c 'import torch.utils; print(torch.utils.cmake_prefix_path)')"
cmake .. 
ccmake -i .. (set the paths)
make install
make PythonInstall

openmm-torch_env.zip