How to install plugin from conda?

[tjrong123]

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]

Can you post the outputs from the following two commands?

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

[tjrong123]

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]

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?