MosaikJump stalls

[GoogleCodeExporter]

What steps will reproduce the problem?
1. MosaikBuild -fr <reference FASTA> -oa [.dat file] -ga [name of ref]
2. MosaikJump -ia [*.dat file from MosaikBuild] -out [jump filename stub] -hs 15
3.

What is the expected output? What do you see instead?

MosaikBuild worked just fine.  The problem occurs with MosaikJump.

MosaikJump will begin hashing the reference sequence.  It gets to 10% 
completion, and then stalls.  After that, the stdout|stderr output is nothing 
but:

10% [==>                                 ]    0.0000 hashes/s       ETA  0 s 

I tried running MosaikJump with -mem 8 .  It gets to 41% completion, and then 
stalls.  The stdout|stderr output once it stalls is just:

41% [==============>                     ]    0.0000 hashes/s       ETA  0 s 

What version of the product are you using? On what operating system?

v. 2.2.3, on Linux CentOS release 6.5

Please provide any additional information below.

The reference I am trying to hash consists of 2.6 Gbase of bacterial genomic 
sequences.  There are 929 bacterial genomic sequences in this reference.

I can send the output of MosaikJump to you, if that is helpful; I can also send 
the bacterial genomic seqs.

Original issue reported on code.google.com by df612...@gmail.com on 5 Jun 2014 at 7:17

[GoogleCodeExporter]

I found if I split up my reference set into several smaller 
sets, MosaikJump won't stall.

But, instead, MosaikJump now crashes with a Segementation 
fault.

At the time it crashes it was doing the step "writing jump 
positions database:" and crashes after completing 50%.

Any ideas on how to get around this problem?

Original comment by df612...@gmail.com on 9 Jun 2014 at 3:40

[GoogleCodeExporter]

After a lot of trial and error, I figured out the problem.

/tmp is too small.  Because of the way the computers I am working on are 
configured, I couldn't see what was happening in /tmp and had no idea it was 
filling up.

The "export MOSAIK_TMP=/newTmpDir" worked.

Original comment by df612...@gmail.com on 19 Jun 2014 at 8:42

[GoogleCodeExporter]

I got the same problem
I am using Liux 64-bit, Mosaik version 2.1.73, internal memory is 512GB,

Using following command lines
export MOSAIK_TMP=/newTmpDir
MosaikJump -ia reference_genome.dat -out reference_genome_15 -hs 15 -mem 1

It runs with only -mem 1 or removing this parameter from command line. I both 
cases, fails to write jump positions in the data bases and says 
segmentation fault (core dumped)

I get following error when I use any other value of -mem
what():  std::bad_alloc
Aborted
I will be thankful for any help or suggestion.

Original comment by luqman....@gmail.com on 11 Jul 2014 at 3:16