0000329: Failed attempt to lock file on networked file system hangs indefinitely, instead of timing out/returning a descriptive error mes

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Date Submitted

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0000329

MEGA

Main Form

public

2016-12-05 09:55

2017-01-20 13:54

Reporter

guest

Assigned To

gstecher

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

assigned

Resolution

open

Platform

Linux

Product Version

MEGA-CC 11 (command line version)

Target Version

Fixed in Version

Summary

0000329: Failed attempt to lock file on networked file system hangs indefinitely, instead of timing out/returning a descriptive error mes

Description

Failed attempt to lock file on networked file system hangs indefinitely, instead of timing out/returning a descriptive error message.

Steps To Reproduce

Try to run an analysis with input/output on a networked filesystem.

Additional Information

The full command line was:

/home/tue39618/EP/Programs/megacc -a /home/tue39618/EP/Programs/Living_seq_Poisson_G5.mao -d /home/tue39618/EP/Test_data/NM_002773/seqs/gene_012.fas -t /home/tue39618/EP/Test_data/NM_002773/trees/gene_012.nwk -o /home/tue39618/EP/Test_data/NM_002773/AS/gene_012.results

This runs perfectly fine on the head node (i.e. it start processing things and spitting out updates). It fails on all of the compute nodes. There, it simply prints the header

MEGA-CC 7.0.18 Molecular Evolutionary Genetics Analysis
Build#: 7160617-x86_64

and then hangs, chewing CPU.

So, I ran it in strace as root on a compute node, and the problem was quickly apparent.

strace /home/tue39618/EP/Programs/megacc -a /home/tue39618/EP/Programs/Living_seq_Poisson_G5.mao -d /home/tue39618/EP/Test_data/NM_002773/seqs/gene_012.fas -t /home/tue39618/EP/Test_data/NM_002773/trees/gene_012.nwk -o /home/tue39618/EP/Test_data/NM_002773/AS/gene_012.results
execve("/home/tue39618/EP/Programs/megacc", ["/home/tue39618/EP/Programs/megac"..., "-a", "/home/tue39618/EP/Programs/Livin"..., "-d", "/home/tue39618/EP/Test_data/NM_0"..., "-t", "/home/tue39618/EP/Test_data/NM_0"..., "-o", "/home/tue39618/EP/Test_data/NM_0"...], [/* 49 vars */]) = 0
brk(0) = 0x21ce000

<SNIP>
A bunch of stuff loading the shared libraries, registering interrupt handlers, mapping memory, and other initialization things
</SNIP>

stat("/home/tue39618/EP/Test_data/NM_002773/AS/gene_012.results", 0x7ffe682a7488) = -1 ENOENT (No such file or directory)
stat("/home/tue39618/EP/Test_data/NM_002773/AS/", {st_mode=S_IFDIR|0775, st_size=4096, ...}) = 0
stat("/home/tue39618/EP/Test_data/NM_002773/AS/", {st_mode=S_IFDIR|0775, st_size=4096, ...}) = 0
access("/home/tue39618/EP/Programs/Living_seq_Poisson_G5.mao", F_OK) = 0
write(1, "MEGA-CC 7.0.18 Molecular Evoluti"..., 56MEGA-CC 7.0.18 Molecular Evolutionary Genetics Analysis
) = 56
write(1, "Build#: 7160617-x86_64\n", 23Build#: 7160617-x86_64
) = 23
access("/home/tue39618/EP/Programs/Living_seq_Poisson_G5.mao", F_OK) = 0
access("/home/tue39618/EP/Programs/Living_seq_Poisson_G5.mao", F_OK) = 0
open("/home/tue39618/EP/Programs/Living_seq_Poisson_G5.mao", O_RDONLY|O_LARGEFILE) = 3
flock(3, LOCK_SH|LOCK_NB

So, the output file doesn't exist (not an error). It writes the header, then goes on to parse the .mao file. This file exists, and is opened with file descriptor 3. Then, the attempt to lock the file hangs.

But, flock isn't safe on NFS mounts (i.e. it doesn't work), and user data is mounted NFS on the compute nodes. This attempt to lock just hangs. It never times out (in my impatient waiting at least), and never returns.

So, this is an issue with this version of megacc accessing files over NFS.

Notes
(0000255) gstecher (administrator) 1969-12-31 17:33	I\'m not sure if this is a bug. Probably trying to open M3 mts files with old versions.

Issue History
Date Modified	Username	Field	Change
2016-12-05 09:55	guest	New Issue
2016-12-05 11:38	gstecher	File Deleted: MEGA3 Error Report.txt
2017-01-20 13:54	gstecher	Assigned To	=> gstecher
2017-01-20 13:54	gstecher	Status	new => assigned

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