MPI version installation error

[shaman-narayanasamy]

Dear authors,

It is me again :)

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

[lmrodriguezr]

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).