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openmm / openmm-plumed

OpenMM plugin to interface with PLUMED
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How to install plugin from conda? #77

Open tjrong123 opened 5 months ago

tjrong123 commented 5 months ago

I have tried to install openmmplumed plugin V1 and V2 using conda. But both of them giving error "no module named openmmplumed". Does the installation require cmake compilation? My openmm version is 8.0. Thanks in advance.

peastman commented 5 months ago

Can you post the outputs from the following two commands?

conda list
python -c "import openmm; print(openmm.pluginLoadedLibNames); print(openmm.Platform.getPluginLoadFailures())"
tjrong123 commented 5 months ago

Hi @peastman , here are the output (thanks a lot!)

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge astunparse 1.6.3 pyhd8ed1ab_0 conda-forge blosc 1.21.5 h0f2a231_0 conda-forge bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.25.0 hd590300_0 conda-forge c-blosc2 2.12.0 hb4ffafa_0 conda-forge ca-certificates 2023.11.17 hbcca054_0 conda-forge cmake 3.28.1 hcfe8598_0 conda-forge cudatoolkit 11.8.0 h4ba93d1_12 conda-forge fftw 3.3.10 nompi_hc118613_108 conda-forge gawk 5.3.0 ha916aea_0 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gmp 6.3.0 h59595ed_0 conda-forge gsl 2.7 he838d99_0 conda-forge hdf5 1.14.3 nompi_h4f84152_100 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.21.2 h659d440_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge libaec 1.1.2 h59595ed_1 conda-forge libblas 3.9.0 20_linux64_openblas conda-forge libcblas 3.9.0 20_linux64_openblas conda-forge libcurl 8.5.0 hca28451_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h807b86a_3 conda-forge libgfortran-ng 13.2.0 h69a702a_3 conda-forge libgfortran5 13.2.0 ha4646dd_3 conda-forge libgomp 13.2.0 h807b86a_3 conda-forge liblapack 3.9.0 20_linux64_openblas conda-forge libnghttp2 1.58.0 h47da74e_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge libsqlite 3.44.2 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libuv 1.46.0 hd590300_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libzlib 1.2.13 hd590300_5 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge lzo 2.10 h516909a_1000 conda-forge mdtraj 1.9.9 py311h90fe790_1 conda-forge mpfr 4.2.1 h9458935_0 conda-forge ncurses 6.4 h59595ed_2 conda-forge nomkl 1.0 h5ca1d4c_0 conda-forge numexpr 2.8.8 py311h039bad6_100 conda-forge numpy 1.26.3 py311h64a7726_0 conda-forge ocl-icd 2.3.1 h7f98852_0 conda-forge ocl-icd-system 1.0.0 1 conda-forge openmm 8.0.0 py311h9766050_4 conda-forge openmm-plumed 1.0 py311h4168a3b_10 conda-forge openssl 3.2.0 hd590300_1 conda-forge packaging 23.2 pyhd8ed1ab_0 conda-forge pandas 2.2.0 py311h320fe9a_0 conda-forge pip 23.3.2 pyhd8ed1ab_0 conda-forge plumed 2.7.3 nompi_h8de8e23_100 conda-forge py-cpuinfo 9.0.0 pyhd8ed1ab_0 conda-forge pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge pytables 3.9.2 py311h10c7f7f_1 conda-forge python 3.11.7 hab00c5b_1_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-tzdata 2023.4 pyhd8ed1ab_0 conda-forge python_abi 3.11 4_cp311 conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge readline 8.2 h8228510_1 conda-forge rhash 1.4.4 hd590300_0 conda-forge scipy 1.11.4 py311h64a7726_0 conda-forge setuptools 69.0.3 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.10 h9fff704_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tzdata 2023d h0c530f3_0 conda-forge wheel 0.42.0 pyhd8ed1ab_0 conda-forge xdrfile 1.1.4 h7f98852_1 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zlib-ng 2.0.7 h0b41bf4_0 conda-forge zstd 1.5.5 hfc55251_0 conda-forge

python -c "import openmm; print(openmm.pluginLoadedLibNames); print(openmm.Platform.getPluginLoadFailures())"

'/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMCPU.so', '/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMPME.so', '/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMCUDA.so', '/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMOpenCL.so', '/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMRPMDCUDA.so', '/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMDrudeCUDA.so', '/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMAmoebaCUDA.so', '/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMRPMDOpenCL.so', '/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMDrudeOpenCL.so', '/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMAmoebaOpenCL.so', '/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMCudaCompiler.so', '/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMRPMDReference.so', '/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMDrudeReference.so', '/home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins/libOpenMMAmoebaReference.so') ()

peastman commented 5 months ago

That's a bit confusing. Conda reports that openmm-plumed is installed, but OpenMM doesn't report either that the plugin was loaded or that an error occurred trying to load it.

The output shows that plugins are being loaded from /home/cbr01/opt/localcolabfold/colabfold-conda/lib/plugins. Can you list the files in that directory to check whether the PLUMED plugin is present or not? And to confirm what it implies: you are working in the base environment (not a different environment you created separately) of a copy of miniconda installed in /home/cbr01/opt/localcolabfold/colabfold-conda. Is that correct?