I was trying to run the latest version of ALLPATHS-LG on our cluster for several times. But my jobs always failed at the same point that is running the RemoveDodgyReads job. The error message I got (shown as below) from RemoveDodgyReads.out file seems showing that my job ran into some memory issues. But our machine has about 500GB memory and the overall memory usage of my job before it failed was only 198GB, so the memory size should not be an issue. I really have no idea how to solve this problem and hope someone can provide some advice. Thanks a lot.
--wls
****************************************************************
Call to new failed, memory usage before call = 198027084k.
Here is the output of top:
Aborting.
Wed Dec 12 08:39:58 2012. Abort. Stopping.
Generating a backtrace...
Dump of stack:
0. CRD::exit(int), in Exit.cc:49
1. our_new_handler(), in RunTime.cc:577
2. Mempool:reAllocate(unsigned long), in Mempool.cc:92
3. Mempool:reAllocate(unsigned long, unsigned long), in Mempool.h:59
4. MempoolAllocator<unsigned char>:reAllocate( ... ), in Mempool.h:243
5. MasterVec<SerfVec<unsigned char> >:reAlloc( ... ), in MasterVec.h:296
--wls
****************************************************************
Call to new failed, memory usage before call = 198027084k.
Here is the output of top:
Aborting.
Wed Dec 12 08:39:58 2012. Abort. Stopping.
Generating a backtrace...
Dump of stack:
0. CRD::exit(int), in Exit.cc:49
1. our_new_handler(), in RunTime.cc:577
2. Mempool:reAllocate(unsigned long), in Mempool.cc:92
3. Mempool:reAllocate(unsigned long, unsigned long), in Mempool.h:59
4. MempoolAllocator<unsigned char>:reAllocate( ... ), in Mempool.h:243
5. MasterVec<SerfVec<unsigned char> >:reAlloc( ... ), in MasterVec.h:296
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