# Glibc error with pre.cluster
**URL:** https://forum.mothur.org/t/glibc-error-with-pre-cluster/20075
**Category:** mothur bugs
**Created:** [August 20, 2019, 4:17pm UTC](https://forum.mothur.org/t/glibc-error-with-pre-cluster/20075 "2019-08-20T16:17:27Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@wolfgangrumpf](https://forum.mothur.org/u/wolfgangrumpf)
#### Post date: [August 20, 2019, 4:17pm UTC](https://forum.mothur.org/t/glibc-error-with-pre-cluster/20075/1 "2019-08-20T16:17:27Z")
I’m analyzing a dataset with 12 groups and on the order of half a million sequences. When I get to the pre.cluster step I have to ramp down the number of processors significantly to get pre.cluster to complete. For example, on a 48-core system with 1.5Tb RAM, if I try to use all 48 processors I get:
\*\*\* glibc detected \*\*\* mothur: double free or corruption (fasttop): 0x00002ae840003280 \*\*\*
======= Backtrace: =========
/opt/glibc-2.14/build/lib/libc.so.6(+0x7374e)[0x2ae81440c74e]
/opt/glibc-2.14/build/lib/libc.so.6(cfree+0x6c)[0x2ae81441074c]
/act/gcc-4.9.2/lib64/libstdc++.so.6(\_ZNSs6assignERKSs+0x87)[0x2ae813a94107]
mothur[0x41b1e3]
mothur[0x85064c]
mothur[0xcbcaa9]
mothur[0x13d991f]
/opt/glibc-2.14/build/lib/libpthread.so.0(+0x6e2b)[0x2ae814182e2b]
/opt/glibc-2.14/build/lib/libc.so.6(clone+0x6d)[0x2ae81447131d]
======= Memory map: ========
00400000-016c0000 r-xp 00000000 00:13 32755946 /gpfs0/export/opt/mothur/1.42.3/mothur
018bf000-018c1000 r–p 012bf000 00:13 32755946 /gpfs0/export/opt/mothur/1.42.3/mothur
018c1000-018c7000 rw-p 012c1000 00:13 32755946 /gpfs0/export/opt/mothur/1.42.3/mothur
With fewer and fewer processors I get part of the analysis to complete, e.g. with 20:
Using 20 processors.
Reducing processors to 12.
/\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*/
Running command: split.groups(groups=lbc10, fasta=combined.good.unique.good.good.filter.unique.fasta, count=combined.good.unique.good.good.filter.count\_table)
/\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*/
Running command: split.groups(groups=lbc9, fasta=combined.good.unique.good.good.filter.unique.fasta, count=combined.good.unique.good.good.filter.count\_table)
/\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*/
Running command: split.groups(groups=libc11, fasta=combined.good.unique.good.good.filter.unique.fasta, count=combined.good.unique.good.good.filter.count\_table)
/\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*/
Running command: split.groups(groups=libc12, fasta=combined.good.unique.good.good.filter.unique.fasta, count=combined.good.unique.good.good.filter.count\_table)
/var/spool/slurmd/job1933416/slurm\_script: line 101: 23939 Aborted (core dumped) mothur mothurpacbio-multisample.sop
The analysis only completes if I ramp it down to 2 processors. At no point in time does the RAM consumption ever appear to be anywhere approaching the available ram. Any ideas why this would happen?
---
### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [August 22, 2019, 7:02pm UTC](https://forum.mothur.org/t/glibc-error-with-pre-cluster/20075/2 "2019-08-22T19:02:43Z")
I think this is related to a race condition we found in the current file class. Are you seeing this with the 1.43.0 beta version?
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### Author:  [@system](https://forum.mothur.org/u/system)
#### Post date: [September 1, 2019, 7:11pm UTC](https://forum.mothur.org/t/glibc-error-with-pre-cluster/20075/3 "2019-09-01T19:11:50Z")
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