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The install for the regular version of nonpareil. I am now attempting the install of nonpareil-mpi. However, below is the error that I receive:
$ make nonpareil-mpi
cd enveomics/ && make nonpareil-mpi
make[1]: Entering directory '/mnt/gaiagpfs/projects/ecosystem_biology/local_tools/nonpareil/enveomics'
mpic++ -DENVEOMICS_MULTI_NODE universal.cpp -c -Wall -std=c++11
mpic++ -DENVEOMICS_MULTI_NODE multinode.cpp -c -Wall -std=c++11
multinode.cpp: In function ‘void init_multinode(int&, char**&, int&, int&)’:
multinode.cpp:16:4: error: ‘MPI’ has not been declared
MPI::Init(argc, argv);
^~~
multinode.cpp:17:16: error: ‘MPI’ has not been declared
processes = MPI::COMM_WORLD.Get_size();
^~~
multinode.cpp:18:16: error: ‘MPI’ has not been declared
processID = MPI::COMM_WORLD.Get_rank();
^~~
multinode.cpp: In function ‘void finalize_multinode()’:
multinode.cpp:21:4: error: ‘MPI’ has not been declared
MPI::Finalize();
^~~
multinode.cpp: In function ‘void barrier_multinode()’:
multinode.cpp:25:4: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Barrier();
^~~
multinode.cpp: In function ‘size_t broadcast_int(size_t)’:
multinode.cpp:31:4: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Bcast(buffer, 1, MPI::INT, 0);
^~~
multinode.cpp:31:37: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Bcast(buffer, 1, MPI::INT, 0);
^~~
multinode.cpp: In function ‘double broadcast_double(double)’:
multinode.cpp:40:4: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Bcast(buffer, 1, MPI::DOUBLE, 0);
^~~
multinode.cpp:40:37: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Bcast(buffer, 1, MPI::DOUBLE, 0);
^~~
multinode.cpp: In function ‘char* broadcast_char(char*, size_t)’:
multinode.cpp:47:4: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Bcast(value, size, MPI::CHAR, 0);
^~~
multinode.cpp:47:39: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Bcast(value, size, MPI::CHAR, 0);
^~~
multinode.cpp: In function ‘char broadcast_char(char)’:
multinode.cpp:53:4: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Bcast(buffer, 1, MPI::CHAR, 0);
^~~
multinode.cpp:53:37: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Bcast(buffer, 1, MPI::CHAR, 0);
^~~
multinode.cpp: In function ‘void reduce_sum_int(int*, int*, int)’:
multinode.cpp:60:4: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Reduce(send, receive, size, MPI::INT, MPI::SUM, 0);
^~~
multinode.cpp:60:48: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Reduce(send, receive, size, MPI::INT, MPI::SUM, 0);
^~~
multinode.cpp:60:58: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Reduce(send, receive, size, MPI::INT, MPI::SUM, 0);
^~~
multinode.cpp: In function ‘void reduce_sum_int(int, int)’:
multinode.cpp:65:4: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Reduce(send_ar, receive_ar, 1, MPI::INT, MPI::SUM, 0);
^~~
multinode.cpp:65:51: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Reduce(send_ar, receive_ar, 1, MPI::INT, MPI::SUM, 0);
^~~
multinode.cpp:65:61: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Reduce(send_ar, receive_ar, 1, MPI::INT, MPI::SUM, 0);
^~~
multinode.cpp: In function ‘void reduce_sum_double(double*, double*, int)’:
multinode.cpp:70:4: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Reduce(send, receive, size, MPI::DOUBLE, MPI::SUM, 0);
^~~
multinode.cpp:70:48: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Reduce(send, receive, size, MPI::DOUBLE, MPI::SUM, 0);
^~~
multinode.cpp:70:61: error: ‘MPI’ has not been declared
MPI::COMM_WORLD.Reduce(send, receive, size, MPI::DOUBLE, MPI::SUM, 0);
^~~
Makefile:32: recipe for target 'nonpareil-mpi' failed
make[1]: *** [nonpareil-mpi] Error 1
make[1]: Leaving directory '/mnt/gaiagpfs/projects/ecosystem_biology/local_tools/nonpareil/enveomics'
Makefile:29: recipe for target 'nonpareil-mpi' failed
make: *** [nonpareil-mpi] Error 2
Below is the MPI version available on my cluster.
$ mpic++ --version
g++ (GCC) 6.3.0
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Let me know if you need more information. It would be nice to implement the mpi version of the tool.
Best regards,
Shaman
The text was updated successfully, but these errors were encountered:
I believe the problem is missing libraries on your machine. Which OS are you using? If you have apt-get you can do:
sudo apt-get install libopenmpi-dev
Note that since Nonpareil v3.0 there is a new kmer-based kernel available (-T kmer) that makes computations much faster, but does not support MPI. MPI can only be used with the traditional alignment kernel (-T alignment).
I have now switched out of deprecated MPI C++ bindings to the stable C bindings since v3.5, and this should be fully solved now. Please feel free to reopen if you continue to experience any issues.
Dear authors,
It is me again :)
The install for the regular version of
nonpareil
. I am now attempting the install ofnonpareil-mpi
. However, below is the error that I receive:Below is the MPI version available on my cluster.
Let me know if you need more information. It would be nice to implement the mpi version of the tool.
Best regards,
Shaman
The text was updated successfully, but these errors were encountered: