mpiBLAST: Open-Source Parallel BLAST

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Installation Guide for mpiBLAST-1.6.0

Note: For other versions, please see the INSTALL file shipped in the mpiBLAST package for installation instructions.


Installation for Unix/Linux/BSD/MacOS X

There are four main steps to installing mpiBLAST from source.

  1. Install MPI (if not already installed)
  2. Download and extract mpiBLAST
  3. Compile and install mpiBLAST
  4. Configure mpiBLAST by editing the ~/.ncbirc file

Each of these steps are described in more detail below.

1) MPI installation

Two popular free versions of MPI are MPICH2 and Open MPI. A successful installation of either is sufficient for mpiBLAST to work. Many OS vendors bundle either MPICH2 or Open MPI with the system, making an installation from source unnecessary.

2) Download and extract mpiBLAST and the matching NCBI Toolbox release

2a) Download mpiBLAST from downloads

2b) Extract mpiBLAST
tar -xvzf mpiBLAST-x.y.z.tgz
or
tar -xvjf mpiBLAST-x.y.z.tbz

3) Compile and install mpiBLAST

3a) Change to the directory containing mpiBLAST
cd /path/to/mpiBLAST-x.y.z
(most likely the command will simply be cd mpiBLAST-x.y.z)

3b) Prepare platform-depdent make files for compiling NCBI BLAST (currently only applicable to IBM Blue Gene systems).
If you are installing mpiBLAST on IBM Blue Gene/L, please review ./ncbi/platform/bluegenel.ncbi.mk and make sure that the compiling configuration (i.e., variables NCBI_AR, NCBI_CC, NCBI_CFLAGS1, NCBI_LDFLAGS1) matches your environment. The configuration file is ./ncbi/platform/bluegenep.ncbi.mk for Blue Gene/P systems.

3c) Configure mpiBLAST

General Unix systems:
./configure

IBM Blue Gene/L systems:
./configure ARCH=bluegenel --host=powerpc64-unknown-linux-gnu

IBM Blue Gene/P systems:
./configure ARCH=bluegenep

Useful extra options to 'configure' in addition to the standard configure flags:

  • --prefix=/path/to/installation/directory
    Specifies the location where mpiBLAST should be installed. (Default is /usr/local/)
  • --with-mpi=/path/to/mpi
    Specifies location of MPI headers and libraries.
  • CONFIG_LIBC macro
    Specifies the path of the C runtime library. mpiBLAST needs to hijack the output function "fwrite" in the C runtime library, which is assumed to be "libc.so.6" by default. Configure this macro when a different libc is used on your platform.
    • The following error message will be reported by mpiBLAST if the libc is not configured properly:
      "Error opening C runtime library: libc.so.6. Use CONFIG_LIBC in the configure script to specify the correct libc."
    • You may consult the system administrator to find out the correct libc. Or you can use "ldd" to search the libc on Linux like operating systems. Go to the src directory under mpiblast-x.y.z, typing "ldd mpiblast" will give you a list of depended shared libraries. An example output on the SGI Alitx is like:
      linux-gate.so.1 => (0xa000000000000000)
      libpthread.so.0 => /lib/libpthread.so.0 (0x200000000005c000)
      libdl.so.2 => /lib/libdl.so.2 (0x200000000010c000)
      libmpi.so => /usr/lib/libmpi.so (0x2000000000124000)
      libmpi++.so => /usr/lib/libmpi++.so (0x2000000003ba4000)
      libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x2000000003c08000)
      libm.so.6.1 => /lib/libm.so.6.1 (0x2000000003d7c000)
      libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x2000000003e30000)
      libc.so.6.1 => /lib/libc.so.6.1 (0x2000000003e60000)
      /lib/ld-linux-ia64.so.2 (0x2000000000000000)
      librt.so.1 => /lib/librt.so.1 (0x2000000004098000)
      It suggests libc.so.6.1 is likely to be the libc being used. Rebuild mpiBLAST by adding CONFIG_LIBC to the configure options:
      ./configure CONFIG_LIBC=libc.so.6.1 ...

3d) Build NCBI libraries
mak ncbi

3e) Build mpiBLAST
make

3f) Install mpiBLAST
make install
(If the --prefix configure option wasn't used then mpiBLAST will be placed in /usr/local and root priveleges will probably be required to install it)

4) Configure mpiBLAST by editing the ~/.ncbirc file

Before running mpiBLAST, it is necessary to configure the shared and local storage paths that each node will use to access the database. A shared storage path is usually a path to a directory residing on a file server, such as NFS, AFS, or samba. The local storage path is typically a subdirectory within the /tmp directory, e.g. /tmp/mpiblast. As worker nodes search the database, they will copy fragments to the local storage directory. During subsequent searches of the same database, the fragments will already reside in local storage and thus will not need to be copied. Note that diskless nodes can be supported by setting the local storage path to be the same as the shared storage path. To configure mpiBLAST create a .ncbirc file in your home directory that looks like:

[NCBI]
Data=/path/to/mpiBLAST-x.y.z/ncbi/data

[BLAST]
BLASTDB=/path/to/shared/storage
BLASTMAT=/path/to/mpiBLAST-x.y.z/ncbi/data

[mpiBLAST]
Shared=/path/to/shared/storage
Local=/path/to/local/storage

The Data variable gives the location of the NCBI Data directory containing BLOSUM and PAM scoring matrices, among other things. The scoring matrix files are necessary for any type of protein BLAST search and should be accessible by all cluster nodes. The BLASTMAT variable also specifies the path to the scoring matrices, and will usually be identical to the Data variable. The BLASTDB variable tells standard NCBI blastall (not mpiBLAST) where to find BLAST databases. As previously mentioned, the Shared and Local variables give the shared and local database paths, respectively. By setting BLASTDB to the same path as Shared, it is possible for NCBI blastall to share the same databases that mpiBLAST uses. In such a configuration, be sure to format all databases with mpiformatdb rather than formatdb.


Installation for Windows

The current release of mpiBLAST, version 1.6.0, is currently unavailable for Windows platforms. Should you wish to obtain a Windows version, please send email to the "developers" mailing list found here: Lists

 
 
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