[Bioclusters] My mpiformatdb can't format NCBI nt DB

[Ron Chen]

Take a look at:
http://www.suse.de/~aj/linux_lfs.html

In short, most programs can be fixed by recompiling
with:
% gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE

 -Ron

--- alfalf <alfalf@hitel.net> wrote:
> Hi.
> 
> I successfully compiled mpiblast in RedHat Linux
> environment with gcc
> version 3.2.
> 
> But, When I perform mpiformatdb with nt sequence
> (about 8.4 GB), mpiformatdb
> print "Error: Unable to open nt" and quit.
> 
> For more information, I perform strace with full
> command.
> 
>  
> 
> ..
> 
> open("/root/.mpiblastrc", O_RDONLY)     = -1 ENOENT
> (No such file or
> directory)
> 
> open("/share/mpiblast/etc/mpiblast.conf", O_RDONLY)
> = 3
> 
> brk(0)                                  = 0x82db000
> 
> brk(0x82dd000)                          = 0x82dd000
> 
> fstat64(3, {st_mode=S_IFREG|0644, st_size=48, ...})
> = 0
> 
> mmap2(NULL, 4096, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) =
> 0x40014000
> 
> read(3, "/path/to/shared/storage\n/path/to"...,
> 8192) = 48
> 
> read(3, "", 4096)                       = 0
> 
> close(3)                                = 0
> 
> munmap(0x40014000, 4096)                = 0
> 
> open("nt", O_RDONLY)                    = -1 EFBIG
> (File too large)
> 
> write(2, "E", 1E)                        = 1
> 
> write(2, "r", 1r)                        = 1
> 
> write(2, "r", 1r)                        = 1
> 
> write(2, "o", 1o)                        = 1
> 
> write(2, "r", 1r)                        = 1
> 
> write(2, ":", 1:)                        = 1
> 
> ..
> 
> write(2, "\n", 1
> 
> )                       = 1
> 
> _exit(-1)                               = ?
> 
>  
> 
> I think that is large file problem. How I can
> perform mpiformatdb with large
> file?
> 
> 


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