Weird behavior of Molfile with dump molfile command

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1

Hi devs and community of LAMMPS

First of all, thank you for the powerful and versatile code! Awesome Job (with the capitol J)

Recently I was trying to dump a .xml trajectory of my simulation using the dump molfile command, and I encountered some problem. I am using LAMMPS 14May2016.

My command is

                        dump t_xml all molfile 500 traj.xml hoomd /home/federico/programs/sources/library/hoomd-molfile-plugin/LINUXAMD64

and when it runs produced the annoying error

ERROR on proc 0: No suitable molfile plugin found (../dump_molfile.cpp:109)

First of all, I tried others plugin, to understand if something was missing in the path (you never know). However, pdb and dcd were working fine, and I was able to write and read these files.
I tried with vaspxml, but I got the same error.

I tried to hack my way in the code, and I find out that the hoomd plugin, and only that one, cannot be opened by dlopen in molfile_interface.cpp.

by inserting the command

     if(!dlopen(fname, RTLD_NOW))
                std::cout << fname << ' ' << dlerror() << std::endl;

I got

     /home/federico/programs/sources/library/hoomd-molfile-plugin/LINUXAMD64/hoomdplugin.so libexpat.so.0: cannot open shared object file: No such file or directory
  
Which is weird, since all the other plugin can be opened. For no apparent reason (to me) if I try to use vaspxml, the plug-in is open with dlopen, but the code answer again

ERROR on proc 0: No suitable molfile plugin found (../dump_molfile.cpp:109)

I tried to reinstall the MOLFILE plug-ins but with no luck. I am using the header of VMD 1.9.2 and not those in the original package of LAMMPS.

I also have a large number of trajs to convert in .xml (~200 files), and I was planning to use LAMMPS, by reading and writing with molfile.

So the question is: Am I doing something weird? Is the molfile plug-ins that I have? Or is it something weird with LAMMPS?

Thank you very much for the code and the support!

F.

2

Hi devs and community of LAMMPS

First of all, thank you for the powerful and versatile code! Awesome Job (with the capitol J)

Recently I was trying to dump a .xml trajectory of my simulation using the dump molfile command, and I encountered some problem. I am using LAMMPS 14May2016.

My command is

                        dump t_xml all molfile 500 traj.xml hoomd /home/federico/programs/sources/library/hoomd-molfile-plugin/LINUXAMD64

and when it runs produced the annoying error

ERROR on proc 0: No suitable molfile plugin found (../dump_molfile.cpp:109)

First of all, I tried others plugin, to understand if something was missing in the path (you never know). However, pdb and dcd were working fine, and I was able to write and read these files.
I tried with vaspxml, but I got the same error.

I tried to hack my way in the code, and I find out that the hoomd plugin, and only that one, cannot be opened by dlopen in molfile_interface.cpp.

by inserting the command

     if(!dlopen(fname, RTLD_NOW))
                std::cout << fname << ' ' << dlerror() << std::endl;

I got

     /home/federico/programs/sources/library/hoomd-molfile-plugin/LINUXAMD64/hoomdplugin.so libexpat.so.0: cannot open shared object file: No such file or directory

Which is weird, since all the other plugin can be opened. For no apparent reason (to me) if I try to use vaspxml, the plug-in is open with dlopen, but the code answer again

this is not weird at all.

ERROR on proc 0: No suitable molfile plugin found (../dump_molfile.cpp:109)

I tried to reinstall the MOLFILE plug-ins but with no luck. I am using the header of VMD 1.9.2 and not those in the original package of LAMMPS.

I also have a large number of trajs to convert in .xml (~200 files), and I was planning to use LAMMPS, by reading and writing with molfile.

So the question is: Am I doing something weird? Is the molfile plug-ins that I have? Or is it something weird with LAMMPS?

you are doing something unusual. you are trying to load a plugin that
is not self-contained, but requires a particular non-standard library.
most molfile plugins simply require the standard c/c++ libraries,
which tend to be present everywhere in a compatible version.

it should be possible to remedy the situation by setting/expanding the
path in the LD_LIBRARY_PATH variable to include a folder containing a
compatible version of libexpat.so.0.

axel.

3

Thank you Axel for the prompt reply!

Indeed, adding the libexpat.so.0 directory to LD_LIBRARY_PATH fixed the problem.

Thank you very much!

F.