Hello all,
While compiling the src in LIGGGHTS-Public, I am getting the following error.
/usr/bin/ld: warning: libmpi.so.12, needed by /usr/lib/x86_64-linux-gnu//libvtkParallelMPI-6.2.so, not found (try using -rpath or -rpath-link)
size ../lmp_auto
Can anybody please help me with this issue?
Thanks in advance.
Regards,
Tarun
bariksan | Tue, 12/28/2021 - 06:47
I had faced similar
I had faced similar difficulties while installing LIGGGHTS in ubuntu 20.04 LTS. Then I switched back to ubuntu 18.04 LTS and was able to install it.
mschramm | Tue, 12/28/2021 - 19:45
Not an issue with liggghts but your development environment
Hello,
Liggghts is not finding your vtk headers. Double check that you have satisfied the pre-requisites to build liggghts. If you have, then you may need to manually set the header and library locations in Makefile.user.
Narayani | Wed, 12/29/2021 - 18:27
further error
hello! thank you for the tip on the ccflags, it seems to be compiling and now i ave an lmp_mpi , but get the following error
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 12 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 14 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 18 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 31 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 22 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 30 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 26 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 8 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 17 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 2 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 7 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 16 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 36 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 19 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 34 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 23 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 10 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 3 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 11 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 20 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 0 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3abf4) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 28 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 15 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 21 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 29 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 38 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 32 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 39 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 24 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 5 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 1 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 35 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 25 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 37 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 4 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 27 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 9 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 13 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
Rank 33 [Wed Dec 29 22:48:09 2021] [c1-0c0s14n0] Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(110): MPI_Comm_rank(comm=0x0, rank=0xe3a684) failed
PMPI_Comm_rank(67).: Invalid communicator
_pmiu_daemon(SIGCHLD): [NID 00248] [c1-0c0s14n0] [Wed Dec 29 22:48:09 2021] PE RANK 30 exit signal Aborted
[NID 00248] 2021-12-29 22:48:09 Apid 2962949: initiated application termination
mschramm | Wed, 12/29/2021 - 19:10
may need to define LD_LIBRARY
Hello,
Looking at the error, I do not know exactly on how to proceed.
Since you set ccflags for the vtk location, you may need to define where the library is in the system variable LD_LIBRARY.