Error in compiling lammps after interfacing with AENET

[ph21...@smail.iitm.ac.in]

Dear Dr. Artrith and team,

Greetings! I'm new to aenet. Thank you Dr. Artrith and team for develping aenet and opensourcing it.  I downloaded USER-AENET and interfaced with lammps 4Feb2020-version. However, I'm getting the following error (complete error response attached ) when I compile the lammps using "make mpi". Kindly provide any suggestion(s) to proceed further. Kindly let me know if you need further information from my side.

error message: "/usr/bin/ld: ../../lib/aenet/lib/libaenet.so: undefined reference to `dsyr2k_'

/usr/bin/ld: ../../lib/aenet/lib/libaenet.so: undefined reference to `dpotrf_'
/usr/bin/ld: ../../lib/aenet/lib/libaenet.so: undefined reference to `dgemm_'
/usr/bin/ld: ../../lib/aenet/lib/libaenet.so: undefined reference to `dpotrs_'
/usr/bin/ld: ../../lib/aenet/lib/libaenet.so: undefined reference to `dgemv_'
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:89: ../lmp_mpi] Error 1
make[1]: Leaving directory '/home/babuji/Desktop/machine_learning/AGY_aenet_lammps/lammps-4Feb20/src/Obj_mpi'

make: *** [Makefile:217: mpi] Error 2"

Thanks in advance!

Have a nice day!

Regards,

Babuji Dandigunta

PhD scholar | Department of Physics,

Indian Institute of Technology - Madras

[Alexander Urban]

Dear Babuji,

These errors happen during the linking step and indicate that the LAPACK library is not found. The relevant line in the text file that you included is

   mpicxx -g -O3 … -lm -ldl -laenet -llbfgsb -o ../lmp_mpi

where “…” is a long list of object file names.  Indeed, LAPACK is omitted here, I don’t know why.

You could try running the above command manually, adding LAPACK and BLAS as follows:

   mpicxx -g -O3 … -lm -ldl -laenet -llbfgsb -llapack -lblas -o ../lmp_mpi

This expects, of course, that both libraries are available on your machine.  They are straightforward to install if you don’t have them already.

Also, make sure that you compile LAMMPS and aenet with the same compiler settings.  Otherwise, it won’t work.

Best wishes,

Alex

--
Alexander Urban
Assistant Professor
Department of Chemical Engineering
Columbia University
812 Mudd Building, 500 W120th Street, New York, NY 10027
212-854-0105
https://urban-group.cheme.columbia.edu

Columbia Electrochemical Energy Center
https://ceec.engineering.columbia.edu

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<error_response_aenet.txt>

[ph21...@smail.iitm.ac.in]

Dear Dr. Urban,

Thanks a lot for the quick reply. I used the command you suggested and some libraries got installed but I got the following error that "laenet" library is not found. I tried looking for it in the website ( http://ann.atomistic.net/documentation/ ) as well as in the aenet folder in my mahcine but couldn't find any. Could you please suggest how to proceed further.

error message:

babuji@babuji-hp-z2:~/Desktop/machine_learning/AGY_aenet_lammps/lammps-4Feb20/src$ mpicxx -g -O3 -L../../lib/aenet/lib -lm -ldl -laenet -llbfgsb -llapack -lblas -o ../lmp_mpi

/usr/bin/ld: cannot find -laenet: No such file or directory

collect2: error: ld returned 1 exit status

Have a nice day!

Thanks and regards,

Babuji Dandigunta

PhD scholar | Department of Physics

Indian Institute of Technology - Madras

[Alexander Urban]

Dear Babuji,

That’s strange because this was not previously an error.

In any case, the error message indicates that you haven’t compiled aenet as a library yet.  In short, you have to compile aenet with the make target ‘lib’ (make -f … lib), but please see the aenet-LAMMPS documentation for details. Perhaps starting over from scratch and closely following the instructions would be best.

Best regards,

Alex

To view this discussion on the web visit https://groups.google.com/d/msgid/aenet/c3326b51-a5bd-4acc-82b7-e1896eed3eccn%40googlegroups.com.

[ph21...@smail.iitm.ac.in]

Dear Dr. Urban,

I did start over from scratch and everything went well. I was able to run the water example for machine learned potential molecular dynamics in the aenet github page. Thanks a lot for your time and suggestions!

I have a quick question. In the aenet methodology we'll assign single atom energies to each element under the section TYPES in generate.in file. Where do we get these single atom energies from? Do we take molecule (like H2) or crystal (graphene) bulk energy and take average for a single atom, or is there any other way?

Have a nice day!
Thanks and regards,
Babuji Dandigunta

PhD scholar | Department of Physics

Indian Institute of Technology - Madras

[Alexander Urban]

Dear Babuji,

Great that you managed to get it to work!

The "atomic energies" are subtracted from the total energies before the neural network training to reduce the variation in energy scale.  There is no rigorous rule on how to select these energies.  If you take the energies of isolated atoms, you would essentially be training on the cohesive energy.  If you select the energies of the elements in their standard state (per atom), you would instead be training on the standard formation energy.  This mostly doesn’t matter for applications since the atomic energies are added back at the stage of energy prediction.

Best wishes,

Alex Urban

--
Alexander Urban
Assistant Professor
Department of Chemical Engineering
Columbia University
812 Mudd Building, 500 W120th Street, New York, NY 10027
212-854-0105
https://urban-group.cheme.columbia.edu

Columbia Electrochemical Energy Center
https://ceec.engineering.columbia.edu

To view this discussion on the web visit https://groups.google.com/d/msgid/aenet/455bc642-e6a2-41d7-af33-355df94a202bn%40googlegroups.com.

[Artrith, N. (Nong)]

Dear Babuji,

You can take the energy of an H2 molecule or a bulk H2 crystal structure and take the average for a single atom.

Please use the energy (e.g., from DFT, if your H2 database is based on DFT) for one single atom of H in your "generate.in" file when setting up the input file for your system (e.g., H2O) using ænet.

Best,

Nong

Dr. Nongnuch Artrith | Assistant Professor | Utrecht University | Debye Institute of Nanomaterials Science | Materials Chemistry and Catalysis |  David de Wied building | Office 4.66 | Universiteitsweg 99 | Phone: +31-6-28-15-97-99 | n.ar...@uu.nl | Web: https://www.uu.nl/staff/NArtrith and  http://nartrith.atomistic.net |

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Subject: Re: [aenet] Error in compiling lammps after interfacing with AENET