Re: NAMD QM/MM

From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Tue Nov 14 2017 - 11:39:49 CST

Dear Constanza,

>From your output, it is clear that ORCA cannot find the libmpi.so library.
To solve the issue, you should add to your "~/.bashrc" (or similar, if you
use another shell) a line that adds the path to that MPI library to your
LD_LIBRARY_PATH.
For example, for bash, you should add the following to your bashrc file:

export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/path/to/mpi/library/"

You should also check the manual for ORCA to make sure the installation
follows all procedures and suggestions.

Best,
Marcelo

---
Marcelo Cardoso dos Reis Melo
PhD Candidate
Luthey-Schulten Group
University of Illinois at Urbana-Champaign
crdsdsr2_at_illinois.edu
+1 (217) 244-5983
On 14 November 2017 at 10:08, Constanza Galaz Araya <Ercalary_at_hotmail.com>
wrote:
>
> Dear NAMD users, I have the following problem to execute a QM / MM
simulation according to the steps of the recent NAMD QM / MM tutorial
executed by terminal namd2 with the configuration file generated by QwikMD
for minimization, which describes the following error (In this case I am
working with ORCA 3.0.3):
>
> TCL: Minimizing for 100 steps
> Info: List of ranks running QM simulations: 0.
>
/home/zehel/Escritorio/Tesis/NAMDQMMM/orca_3_0_3_linux_x86-64/orca_gtoint_mpi:
error while loading shared libraries: libmpi.so.1: cannot open shared
object file: No such file or directory
>
/home/zehel/Escritorio/Tesis/NAMDQMMM/orca_3_0_3_linux_x86-64/orca_gtoint_mpi:
error while loading shared libraries: libmpi.so.1: cannot open shared
object file: No such file or directory
>
/home/zehel/Escritorio/Tesis/NAMDQMMM/orca_3_0_3_linux_x86-64/orca_gtoint_mpi:
error while loading shared libraries: libmpi.so.1: cannot open shared
object file: No such file or directory
>
/home/zehel/Escritorio/Tesis/NAMDQMMM/orca_3_0_3_linux_x86-64/orca_gtoint_mpi:
error while loading shared libraries: libmpi.so.1: cannot open shared
object file: No such file or directory
>
/home/zehel/Escritorio/Tesis/NAMDQMMM/orca_3_0_3_linux_x86-64/orca_gtoint_mpi:
error while loading shared libraries: libmpi.so.1: cannot open shared
object file: No such file or directory
>
/home/zehel/Escritorio/Tesis/NAMDQMMM/orca_3_0_3_linux_x86-64/orca_gtoint_mpi:
error while loading shared libraries: libmpi.so.1: cannot open shared
object file: No such file or directory
>
/home/zehel/Escritorio/Tesis/NAMDQMMM/orca_3_0_3_linux_x86-64/orca_gtoint_mpi:
error while loading shared libraries: libmpi.so.1: cannot open shared
object file: No such file or directory
>
/home/zehel/Escritorio/Tesis/NAMDQMMM/orca_3_0_3_linux_x86-64/orca_gtoint_mpi:
error while loading shared libraries: libmpi.so.1: cannot open shared
object file: No such file or directory
> ORCA finished by error termination in ORCA_GTOInt
> ERROR: Could not find QM output file!
> FATAL ERROR: No such file or directory
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: No such file or directory
>
> [0] Stack Traceback:
>   [0:0]   [0x142f2be]
>   [0:1]   [0x4fa5ad]
>   [0:2]   [0x57b7b4]
>   [0:3]   [0x1280a9c]
>   [0:4]   [0x128100b]
>   [0:5]   [0x1438cc5]
>   [0:6]   [0xeb5714]
>   [0:7] TclInvokeStringCommand+0x88  [0x149aed8]
>   [0:8]   [0x149d9f0]
>   [0:9]   [0x149edd6]
>   [0:10]   [0x149f5b6]
>   [0:11]   [0x15013c1]
>
> I have already tried different configurations and versions of openmpi but
I still have the same library problem, is there someone who has had a
similar problem?
>
> Beforehand thank you very much!

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