Hello,

As I indicated in another thread (#4), I am facing "Segmentation fault" issues when running the cluster module of gmx_clusterByFeatures compiled via Pip3. The compilation is performed without any error with Pip3.

So, I tried to compile gmx_clusterByFeatures via Python or via Cmake. However, the compilation fails in both cases and I obtain the following error:
error.txt
(here for the Python compilation)

For info, I am working on a Linux machine with Python 3.7.4 and GROMACS 1.8.3 without MPI or GPU support.

Thanks for any help.

Hi, I have been using gmx_clusterByFeatures to cluster my trajectory. I want .pdb output and I have specified it on my command line, however I am getting .xtc cluster output. I need to analyse the clusters generated and without a topology it is hard to use .xtc files. How can I get .pdb???

Dear Dr Kumar

I wish you a Happy New Year. Now my questions

For my work I would like to compute the "average" pore radius for a given system for given time period (say 100 - 200 ns) and I have two questions about the outputs of gmx_clusterByFeatures hole program.

1. Are the printed values (lines with the " (sampled) " and "(mid-point) " fields) on display terminal give the "average" pore radius along the z axis for this time period?

2. I understand that -pdb argument of the gmx_clusterByFeatures hole provides the structure of the pore for each time frame (here between 100 ns -- 200 ns) in the PDB format. It is possible to obtain from pdb the "average" structure of the pore (also in the PDB format) for the mentioned time period that can be used, for instance for plotting with Pymol? If yes how

Thank you for your response

Best

Stéphane

:-) gmx_clusterByFeatures cluster (-:

         Author: Rajendra Kumar

   Copyright (C) 2018-2019  Rajendra Kumar

gmx_clusterByFeatures is a free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

gmx_clusterByFeatures is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with gmx_clusterByFeatures. If not, see http://www.gnu.org/licenses/.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

=======================
Cluster Log output

Command:

cluster -s md_0_1.tpr -f md1.xtc -feat proj.xvg -method kmeans -nfeature 20 -cmetric ssr-sst -ncluster 15 -fit2central -sort features -cpdb central.pdb -fout cluster.xtc -plot pca_cluster.png

Reading file md_0_1.tpr, VERSION 2018.2 (single precision)
Reading file md_0_1.tpr, VERSION 2018.2 (single precision)

Choose a group for the output:

Program: cluster, version 2016.5
Source file: src/gromacs/utility/datafilefinder.cpp (line 210)
Function: std::string gmx::DataFileFinder::findFile(const gmx::DataFileOptions&) const

System I/O error:
Library file 'residuetypes.dat' not found in current dir nor in your GMXLIB
path nor in the default directories.
The following paths were searched:
/home/bd422/Desktop/BD/3 (current dir)
/home/bd422/Desktop/BD/3/top
/external/gromacs-2016.5/installed/share/gromacs/top (default)

HI all

I have the data from gmx_clusterByFeatures with the following commands bot in a bash script

/ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/install_noMPI/bin/gmx_clusterByFeatures hole -f /ccc/store/cont003/drf/abel01/MDs_GENCI_2017/GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2/XTC/1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_Along_Z_Axis_Rotated_afterFit_Center.xtc -s 1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_fake_reoriented.tpr -n System.ndx -o 1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_hole_radius_along_Z.dat -pdb 1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_hole_sphpdb.pdb -b 229000 -e 230000 -fit -sample 0.5 -cvect 0 0 1 -rad bondi

And I would like to obtain and image of the results so I use the following command

/ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/install_noMPI/bin/gmx_clusterByFeatures holeplot -i 1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_hole_radius_along_Z.dat -csv 1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_hole_radius_along_Z.csv -xmin 0 -xmax 15 -ax Z -resplot -b 229000 -e 230000 -ymin 0 -ymax 15 --output 1JNO_GrA_65SDS_Micelle_CHARMM36_TIP3P_rep2_hole_radius_along_Z.pdf -fs 14 -dpi 300 -rlsize 10

But I obtain the error and no pdf file is generated
Traceback (most recent call last):
File "/ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/install_noMPI/bin/gmx_clusterByFeatures", line 8, in
gmx_clusterByFeatures.main.main()
File "/ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/gmx_clusterByFeatures-master/gmx_clusterByFeatures/main.py", line 79, in main
holeplot.main()
File "/ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/gmx_clusterByFeatures-master/gmx_clusterByFeatures/holeplot.py", line 170, in main
holeProcessor.plot_radius_residues(outputFile, csvfile=args.outCsvFile, violinplot=args.violinplot,
AttributeError: 'Namespace' object has no attribute 'outCsvFile'

See also the file attached.

Could you help me to resolve this problem

Thank you
GrA_SDS_hole.4602493e.TXT

Sir,
I tried installing gmx_clusterByFeatures using command "sudo pip3 install gmx-clusterByFeatures" on Linux, Ubuntu version- 22.04, Python version- 3.10.4, but it shows the following error:
ERROR: Could not find a version that satisfies the requirement gmx-clusterByFeatures (from versions: none)
ERROR: No matching distribution found for gmx-clusterByFeatures

Kindly help me resolve this issue.

Thank you

Hello,

Thank you for writing this super neat program! I've used it a lot in my project. I'd like to cite this in my manuscript - how do I go about it?

-A

Hi,
I am getting troubles while trying to run dbscan method with gmx_clusterByFeatures: "AttributeError: 'DBSCAN' object has no attribute 'inertia_'"
Any help please.

Hello
I have some issues to compile gmx_clusterByFeatures on a HPC cluster with cmake or python3
I used

• GROMACS 2016.6
• GCC7.3
• Pybind11 (2.4.3)

The compilation seems correct (no error) but the program crashes with a seg fault when I typing

/ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/install/bin/gmx_clusterByFeatures hole -h

##The error message
[cobalt172:04246] *** Process received signal ***
[cobalt172:04246] Signal: Segmentation fault (11)
[cobalt172:04246] Signal code: Address not mapped (1)
[cobalt172:04246] Failing at address: (nil)
[cobalt172:04246] [ 0] /lib64/libpthread.so.0(+0xf5d0)[0x2b8b8ecc45d0]
[cobalt172:04246] [ 1] /opt/mpi/openmpi-icc/2.0.4.4.0.xcea/lib/libopen-pal.so.20(opal_argv_join+0x33)[0x2b8ba11fab93]
[cobalt172:04246] [ 2] /ccc/products/openmpi-2.0.4/intel--17.0.6.256/default/lib/libmpi.so.20(ompi_mpi_init+0xd2e)[0x2b8b9c4add3e]
[cobalt172:04246] [ 3] /ccc/products/openmpi-2.0.4/intel--17.0.6.256/default/lib/libmpi.so.20(PMPI_Init_thread+0x62)[0x2b8b9c4ccab2]
[cobalt172:04246] [ 4] /ccc/work/cont003/drf/abel01/gromacs-2016.6_Cobalt/build_Cobalt/lib64/libgromacs.so.2(_ZN3gmx4initEPiPPPc+0x85)[0x2b8b9b5e38a5]
[cobalt172:04246] [ 5] /ccc/work/cont003/drf/abel01/gromacs-2016.6_Cobalt/build_Cobalt/lib64/libgromacs.so.2(_ZN3gmx18initForCommandLineEPiPPPc+0x19)[0x2b8b9b4a4159]
[cobalt172:04246] [ 6] /ccc/work/cont003/drf/abel01/gromacs-2016.6_Cobalt/build_Cobalt/lib64/libgromacs.so.2(_ZN3gmx24CommandLineModuleManager21runAsMainSingleModuleEiPPcPNS_18ICommandLineModuleE+0x25)[0x2b8b9b4a6b55]
[cobalt172:04246] [ 7] /ccc/work/cont003/drf/abel01/gromacs-2016.6_Cobalt/build_Cobalt/lib64/libgromacs.so.2(_ZN3gmx24CommandLineModuleManager14runAsMainCMainEiPPcPFiiS2_E+0x36)[0x2b8b9b4a6c36]
[cobalt172:04246] [ 8] /ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/install/lib/python3.7/site-packages/gmx_clusterByFeatures-0.1.17-py3.7-linux-x86_64.egg/gmx_clusterByFeatures/gmx_clusterByFeatures.cpython-37m-x86_64-linux-gnu.so(+0x9078c)[0x2b8b9b26278c]
[cobalt172:04246] [ 9] /ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/install/lib/python3.7/site-packages/gmx_clusterByFeatures-0.1.17-py3.7-linux-x86_64.egg/gmx_clusterByFeatures/gmx_clusterByFeatures.cpython-37m-x86_64-linux-gnu.so(+0x8b375)[0x2b8b9b25d375]
[cobalt172:04246] [10] /ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/install/lib/python3.7/site-packages/gmx_clusterByFeatures-0.1.17-py3.7-linux-x86_64.egg/gmx_clusterByFeatures/gmx_clusterByFeatures.cpython-37m-x86_64-linux-gnu.so(+0x96678)[0x2b8b9b268678]
[cobalt172:04246] [11] /ccc/work/cont003/drf/abel01/gmx_clusterByFeatures_Cobalt_suppapp/install/lib/python3.7/site-packages/gmx_clusterByFeatures-0.1.17-py3.7-linux-x86_64.egg/gmx_clusterByFeatures/gmx_clusterByFeatures.cpython-37m-x86_64-linux-gnu.so(+0x934d6)[0x2b8b9b2654d6]
[cobalt172:04246] [12] /ccc/products2/python3-3.7.2/Atos_7__x86_64/intel--17.0.4.196__openmpi--2.0.4/default/lib/libpython3.7m.so.1.0(_PyMethodDef_RawFastCallKeywords+0x31b)[0x2b8b8e834e3b]
[cobalt172:04246] [13] /ccc/products2/python3-3.7.2/Atos_7__x86_64/intel--17.0.4.196__openmpi--2.0.4/default/lib/libpython3.7m.so.1.0(_PyCFunction_FastCallKeywords+0x25)[0x2b8b8e834eb5]
[cobalt172:04246] [14] /ccc/products2/python3-3.7.2/Atos_7__x86_64/intel--17.0.4.196__openmpi--2.0.4/default/lib/libpython3.7m.so.1.0(_PyEval_EvalFrameDefault+0x8095)[0x2b8b8e816ce5]
[cobalt172:04246] [15] /ccc/products2/python3-3.7.2/Atos_7__x86_64/intel--17.0.4.196__openmpi--2.0.4/default/lib/libpython3.7m.so.1.0(+0x69ad0)[0x2b8b8e80dad0]
[cobalt172:04246] [16] /ccc/products2/python3-3.7.2/Atos_7__x86_64/intel--17.0.4.196__openmpi--2.0.4/default/lib/libpython3.7m.so.1.0(_PyEval_EvalFrameDefault+0x8329)[0x2b8b8e816f79]
[cobalt172:04246] [17] /ccc/products2/python3-3.7.2/Atos_7__x86_64/intel--17.0.4.196__openmpi--2.0.4/default/lib/libpython3.7m.so.1.0(_PyEval_EvalCodeWithName+0x9d0)[0x2b8b8e8dfb80]
[cobalt172:04246] [18] /ccc/products2/python3-3.7.2/Atos_7__x86_64/intel--17.0.4.196__openmpi--2.0.4/default/lib/libpython3.7m.so.1.0(PyEval_EvalCodeEx+0x6d)[0x2b8b8e8dfced]
[cobalt172:04246] [19] /ccc/products2/python3-3.7.2/Atos_7__x86_64/intel--17.0.4.196__openmpi--2.0.4/default/lib/libpython3.7m.so.1.0(PyEval_EvalCode+0x3b)[0x2b8b8e8dfd3b]
[cobalt172:04246] [20] /ccc/products2/python3-3.7.2/Atos_7__x86_64/intel--17.0.4.196__openmpi--2.0.4/default/lib/libpython3.7m.so.1.0(+0x162a94)[0x2b8b8e906a94]
[cobalt172:04246] [21] /ccc/products2/python3-3.7.2/Atos_7__x86_64/intel--17.0.4.196__openmpi--2.0.4/default/lib/libpython3.7m.so.1.0(PyRun_FileExFlags+0x9d)[0x2b8b8e908d9d]
[cobalt172:04246] [22] /ccc/products2/python3-3.7.2/Atos_7__x86_64/intel--17.0.4.196__openmpi--2.0.4/default/lib/libpython3.7m.so.1.0(PyRun_SimpleFileExFlags+0xe7)[0x2b8b8e908ef7]
[cobalt172:04246] [23] /ccc/products2/python3-3.7.2/Atos_7__x86_64/intel--17.0.4.196__openmpi--2.0.4/default/lib/libpython3.7m.so.1.0(+0x17f8e7)[0x2b8b8e9238e7]
[cobalt172:04246] [24] /ccc/products2/python3-3.7.2/Atos_7__x86_64/intel--17.0.4.196__openmpi--2.0.4/default/lib/libpython3.7m.so.1.0(_Py_UnixMain+0x2d)[0x2b8b8e923bdd]
[cobalt172:04246] [25] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b8b8f5fc495]
[cobalt172:04246] [26] /ccc/products/python3-3.7.2/intel--17.0.4.196__openmpi--2.0.4/default/bin/python3[0x4007be]
[cobalt172:04246] *** End of error message ***
Segmentation fault

the commands I used to compile the code (see file attached)

compile_commands_Cobalt.TXT

Could you help me to resolve this issue ?

Thank you

Stéphane

Hi,

First and foremost thank you for writing the module for easy MD analysis.
While using the module I have faced some issues, it would be really grateful if you can help me with it.

I was trying to do ligand clustering using gmx_clusterByFeatures cluster option, command has been followed the same as manual.
First generated Proj.xvg file from gromacs PCA and fed to gmx_clusterByFeatures. The command is as follow:

gmx_clusterByFeatures cluster' -s system.tpr -f system-center.xtc -n index.ndx -feat proj.xvg -method kmeans -nfeature 20 -cmetric ssr-sst -ncluster 15 -fit2central -sort features -cpdb central.pdb -fout cluster.xtc -plot pca_cluster.png

So the process ran until I face an error:
Program: gmx_clusterByFeatures cluster, version 2016.5

Standard library runtime error (possible bug):
(exception type: N8pybind1117error_already_setE)
UnboundLocalError: local variable 'plt' referenced before assignment

At:
(137): plotFeaturesClusters
(2):
/usr/local/lib/python3.6/dist-packages/gmx_clusterByFeatures/main.py(59):
main
/usr/local/bin/gmx_clusterByFeatures(8):

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I realized this error is due to the -plot option, cause when I ran the same command without -plot option, run was successful.
But now to plot the pca of cluster, I tried looking gmx_clusterByFeatures featuresplot option.
gmx_clusterByFeatures featuresplot -I input.txt -feat proj.xvg -clid clid.xvg -o out.png
Here we need to provide an -I input.txt,
I didn’t understand how do I generate input.txt, an example is given in manual still I didn’t understand how to generate this input file.

It will be really helpful if you provide me with some help/leads.

Thank you,
A