Opened 11 months ago

Closed 3 hours ago

#864 closed issue (handled)

ARB crashed using build_server in the Admin menu of PT_SERVER

Reported by: guest Owned by: westram
Priority: normal Milestone:
Component: no idea Version: arb-6.x
Keywords: Cc: laurent.toffin@…

Description (last modified by westram)

Hello,

I have to use ARB with a singularity installation (image arb-bio-6.0.6 from Biocontainers) and that version crached when I attempt to build the pt_server.

ARB is starting as follows: singularity exec -B $HOME/arb-bio-6.0.6/pt_server:/usr/local/lib/arb/lib/pts arb-bio-6.0.6.sif arb

Note: since ARB wants to write to a path inside the container, I linked /usr/local/lib/arb/lib/pts to a local path on my cluster.

Now, when building the pt_server, I got that huge error message, see below.

Any idea how to fix that error ?

Best regards, Laurent Toffin, Ifremer 

----
WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Using ARBHOME='/usr/local/lib/arb'
Using properties from /home1/datahome/ltoffin/.arb_prop
Please wait while the program ARB is starting .....
Waiting for '/home1/datahome/ltoffin/.arb_tmp/sockets/arb_launcher.23243'..
find: unrecognized: -cmin
BusyBox v1.22.1 (2014-05-23 01:24:27 UTC) multi-call binary.

Usage: find [-HL] [PATH]... [OPTIONS] [ACTIONS]

Search for files and perform actions on them.
First failed action stops processing of current file.
Defaults: PATH is current directory, action is '-print'

	-L,-follow	Follow symlinks
	-H		...on command line only
	-xdev		Don't descend directories on other filesystems
	-maxdepth N	Descend at most N levels. -maxdepth 0 applies
			actions to command line arguments only
	-mindepth N	Don't act on first N levels
	-depth		Act on directory *after* traversing it

Actions:
	( ACTIONS )	Group actions for -o / -a
	! ACT		Invert ACT's success/failure
	ACT1 [-a] ACT2	If ACT1 fails, stop, else do ACT2
	ACT1 -o ACT2	If ACT1 succeeds, stop, else do ACT2
			Note: -a has higher priority than -o
	-name PATTERN	Match file name (w/o directory name) to PATTERN
	-iname PATTERN	Case insensitive -name
	-path PATTERN	Match path to PATTERN
	-ipath PATTERN	Case insensitive -path
	-regex PATTERN	Match path to regex PATTERN
	-type X		File type is X (one of: f,d,l,b,c,...)
	-perm MASK	At least one mask bit (+MASK), all bits (-MASK),
			or exactly MASK bits are set in file's mode
	-mtime DAYS	mtime is greater than (+N), less than (-N),
			or exactly N days in the past
	-mmin MINS	mtime is greater than (+N), less than (-N),
			or exactly N minutes in the past
	-newer FILE	mtime is more recent than FILE's
	-user NAME/ID	File is owned by given user
	-group NAME/ID	File is owned by given group
	-size N[bck]	File size is N (c:bytes,k:kbytes,b:512 bytes(def.))
			+/-N: file size is bigger/smaller than N
	-prune		If current file is directory, don't descend into it
If none of the following actions is specified, -print is assumed
	-print		Print file name
	-print0		Print file name, NUL terminated
	-exec CMD ARG ;	Run CMD with all instances of {} replaced by
			file name. Fails if CMD exits with nonzero

find: unrecognized: -empty
BusyBox v1.22.1 (2014-05-23 01:24:27 UTC) multi-call binary.

Usage: find [-HL] [PATH]... [OPTIONS] [ACTIONS]

Search for files and perform actions on them.
First failed action stops processing of current file.
Defaults: PATH is current directory, action is '-print'

	-L,-follow	Follow symlinks
	-H		...on command line only
	-xdev		Don't descend directories on other filesystems
	-maxdepth N	Descend at most N levels. -maxdepth 0 applies
			actions to command line arguments only
	-mindepth N	Don't act on first N levels
	-depth		Act on directory *after* traversing it

Actions:
	( ACTIONS )	Group actions for -o / -a
	! ACT		Invert ACT's success/failure
	ACT1 [-a] ACT2	If ACT1 fails, stop, else do ACT2
	ACT1 -o ACT2	If ACT1 succeeds, stop, else do ACT2
			Note: -a has higher priority than -o
	-name PATTERN	Match file name (w/o directory name) to PATTERN
	-iname PATTERN	Case insensitive -name
	-path PATTERN	Match path to PATTERN
	-ipath PATTERN	Case insensitive -path
	-regex PATTERN	Match path to regex PATTERN
	-type X		File type is X (one of: f,d,l,b,c,...)
	-perm MASK	At least one mask bit (+MASK), all bits (-MASK),
			or exactly MASK bits are set in file's mode
	-mtime DAYS	mtime is greater than (+N), less than (-N),
			or exactly N days in the past
	-mmin MINS	mtime is greater than (+N), less than (-N),
			or exactly N minutes in the past
	-newer FILE	mtime is more recent than FILE's
	-user NAME/ID	File is owned by given user
	-group NAME/ID	File is owned by given group
	-size N[bck]	File size is N (c:bytes,k:kbytes,b:512 bytes(def.))
			+/-N: file size is bigger/smaller than N
	-prune		If current file is directory, don't descend into it
If none of the following actions is specified, -print is assumed
	-print		Print file name
	-print0		Print file name, NUL terminated
	-exec CMD ARG ;	Run CMD with all instances of {} replaced by
			file name. Fails if CMD exits with nonzero

[arb_launcher[0]: Starting 'arb_ntree'..]
Using properties from '/usr/local/lib/arb/lib/arb_default/status.arb'
Using properties from '/home1/datahome/ltoffin/.arb_prop/ntree.arb'
ARB_DB_CLIENT_OPEN: AISC_CLIENT-Error: Cannot resolve hostname: 'datarmor2' (h_errno=2='Host name lookup failure')
env: can't execute 'c++filt': No such file or directory

-------------------- ARB-backtrace 'received signal 11':
/usr/local/lib/arb/lib/libCORE.so(_Z18GBK_dump_backtraceP8_IO_FILEPKc+0x26)[0x7fffed3d5f36]
/usr/local/lib/arb/lib/libCORE.so(+0xff34)[0x7fffed3d7f34]
/lib/libc.so.6(+0x354e0)[0x7fffec07c4e0]
/usr/local/lib/arb/lib/libARBDB.so(_Z15gb_save_mapfileP12GB_MAIN_TYPEPKc+0x30a)[0x7fffed67ea3a]
/usr/local/lib/arb/lib/libARBDB.so(_ZN12GB_MAIN_TYPE7save_asEPKcS1_+0x56c)[0x7fffed64238c]
arb_ntree[0x5276de]
/usr/local/lib/arb/lib/libWINDOW.so(_ZN5AW_cb13run_callbacksEv+0x97)[0x7fffecf175c7]
/usr/local/lib/arb/lib/libWINDOW.so(_Z18AW_server_callbackP10_WidgetRecPvS1_+0x99)[0x7fffecf33e29]
/usr/local/lib/arb/bin/../../libXm.so.4(+0x10bc7e)[0x7fffeca87c7e]
/usr/local/lib/arb/bin/../../libXm.so.4(+0x10ba4b)[0x7fffeca87a4b]
/usr/local/lib/arb/bin/../../libXt.so.6(+0x4a72f)[0x7fffed9a972f]
/usr/local/lib/arb/bin/../../libXt.so.6(_XtTranslateEvent+0x32d)[0x7fffed9aa6ed]
/usr/local/lib/arb/bin/../../libXt.so.6(XtDispatchEventToWidget+0x108)[0x7fffed9821b8]
/usr/local/lib/arb/bin/../../libXt.so.6(+0x23c9f)[0x7fffed982c9f]
/usr/local/lib/arb/bin/../../libXt.so.6(XtDispatchEvent+0x152)[0x7fffed982e02]
/usr/local/lib/arb/bin/../../libXt.so.6(XtAppProcessEvent+0x24a)[0x7fffed98ed5a]
/usr/local/lib/arb/bin/../../libXt.so.6(XtAppMainLoop+0x2e)[0x7fffed98323e]
arb_ntree(_Z8ARB_mainiPPc+0x191a)[0x47050a]
/lib/libc.so.6(__libc_start_main+0xf5)[0x7fffec068be5]
arb_ntree[0x449075]
-------------------- End of backtrace
[Terminating with signal 11]
ARB: Loading 'ntree.arb'
ARB: Loading '/home1/datahome/ltoffin/.arb_prop/ntree.arb' done

ARB: ARB: Loading '/home1/datahome/ltoffin/DATABASE/SILVA138/SILVA_138.1_ANME3_SSURef_NR99_12_06_20_opt.arb' + Changes-File /home1/datahome/ltoffin/DATABASE/SILVA138/SILVA_138.1_ANME3_SSURef_NR99_12_06_20_opt.a00
ARB: ARB: no FastLoad File '/home1/datahome/ltoffin/DATABASE/SILVA138/SILVA_138.1_ANME3_SSURef_NR99_12_06_20_opt.ARM' found => loading entire DB
ARB: ARB: Loading '/home1/datahome/ltoffin/DATABASE/SILVA138/SILVA_138.1_ANME3_SSURef_NR99_12_06_20_opt.arb' done

[arb_launcher[0]: 'arb_ntree' has terminated with error 139]
[arb_launcher[0]: All launched processes terminated]
tar: invalid option -- 'z'
BusyBox v1.22.1 (2014-05-23 01:24:27 UTC) multi-call binary.

Usage: tar -[cxthvO] [-X FILE] [-T FILE] [-f TARFILE] [-C DIR] [FILE]...

Create, extract, or list files from a tar file

Operation:
	c	Create
	x	Extract
	t	List
	f	Name of TARFILE ('-' for stdin/out)
	C	Change to DIR before operation
	v	Verbose
	O	Extract to stdout
	h	Follow symlinks
	exclude	File to exclude
	X	File with names to exclude
	T	File with names to include


Session log has been stored in /home1/datahome/ltoffin/.arb_prop/logs/session.20241211_082811.23297.tgz
    and is also accessible via /home1/datahome/ltoffin/ARB_last_session.tgz

ARB crashed :-(
To report this goto http://bugs.arb-home.de/wiki/BugReport
Please include the session log mentioned above

[press ENTER]

Change History (2)

comment:1 Changed 10 months ago by westram

  • Description modified (diff)
  • Owner changed from devel to westram
  • Status changed from new to accepted

Dear Laurent,

the problem may be caused by an invalid hostname definition. The pt-server uses the symbolic hostname 'localhost' to access a pt-server running on the same machine (or to check if any is running).

Try in a terminal window whether 

ping -c 3 localhost

prints something reasonable like 

PING localhost (127.0.0.1) 56(84) bytes of data.
64 bytes from localhost (127.0.0.1): icmp_seq=1 ttl=64 time=0.061 ms
64 bytes from localhost (127.0.0.1): icmp_seq=2 ttl=64 time=0.029 ms
64 bytes from localhost (127.0.0.1): icmp_seq=3 ttl=64 time=0.027 ms

--- localhost ping statistics ---
3 packets transmitted, 3 received, 0% packet loss, time 2035ms
rtt min/avg/max/mdev = 0.027/0.039/0.061/0.015 ms

If doing so results in an error, arb won't work either.

Best regards Ralf

comment:2 Changed 3 hours ago by westram

  • Resolution set to handled
  • Status changed from accepted to closed
  • Type changed from defect to issue

assuming hints helped :-)

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