23 Oct
2013
23 Oct
'13
11:57 a.m.
please see output with 1 thread:
msnoise@seisapp:~/MSNoise-Temp/MSNoise-1.2$ python test.s01scan_archive.py init 1
2013-10-23 10:59:05,935 [INFO] *** Starting: Scan Archive ***
mtime: -1
init man!
will work on 1 threads
/home/msnoise/SDS/2010/3A/L002/HHE.D/3A.L002..HHE.D.2010.089
Traceback (most recent call last):
File "test.s01scan_archive.py", line 204, in <module>
t.start()
File "/home/msnoise/anaconda/lib/python2.7/threading.py", line 743, in start
_start_new_thread(self.__bootstrap, ())
thread.error: can't start new thread
Traceback (most recent call last):
File "_ctypes/callbacks.c", line 314, in 'calling callback
function'
File
"/home/msnoise/anaconda/lib/python2.7/site-packages/obspy-0.8.4-py2.7-linux-i686.egg/obspy/mseed/core.py",
line 261, in allocate_data
data = np.empty(samplecount, dtype=DATATYPES[sampletype])
MemoryError
*** glibc detected *** python: corrupted double-linked list: 0x30fc1a10 ***
======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6(+0x6b161)[0xb74c6161]
/lib/tls/i686/cmov/libc.so.6(+0x6caa3)[0xb74c7aa3]
/lib/tls/i686/cmov/libc.so.6(cfree+0x6d)[0xb74caa9d]
/home/msnoise/anaconda/lib/python2.7/site-packages/obspy-0.8.4-py2.7-linux-i686.egg/obspy/mseed/../lib/libmseed.so(msr_free+0x6c)[0xb01db87c]
/home/msnoise/anaconda/lib/python2.7/site-packages/obspy-0.8.4-py2.7-linux-i686.egg/obspy/mseed/../lib/libmseed.so(readMSEEDBuffer+0x7d1)[0xb01f0bf1]
/home/msnoise/anaconda/lib/python2.7/lib-dynload/_ctypes.so(ffi_call_SYSV+0x1a)[0xb69d325e]
/home/msnoise/anaconda/lib/python2.7/lib-dynload/_ctypes.so(ffi_call+0x63)[0xb69d3093]
/home/msnoise/anaconda/lib/python2.7/lib-dynload/_ctypes.so(_ctypes_callproc+0x3be)[0xb69c7ece]
/home/msnoise/anaconda/lib/python2.7/lib-dynload/_ctypes.so(+0x6dda)[0xb69bfdda]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyObject_Call+0x5c)[0xb75ff1cc]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x110a)[0xb76a465a]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0xb76ab5f2]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(+0x57f3c)[0xb762df3c]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyObject_Call+0x5c)[0xb75ff1cc]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3cdd)[0xb76a722d]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0xb76ab5f2]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(+0x57f3c)[0xb762df3c]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyObject_Call+0x5c)[0xb75ff1cc]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3cdd)[0xb76a722d]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0xb76ab5f2]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(+0x57f3c)[0xb762df3c]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyObject_Call+0x5c)[0xb75ff1cc]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3cdd)[0xb76a722d]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0xb76ab5f2]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(+0x57f3c)[0xb762df3c]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyObject_Call+0x5c)[0xb75ff1cc]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3cdd)[0xb76a722d]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0xb76ab5f2]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x607d)[0xb76a95cd]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0xb76ab5f2]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(+0x57f3c)[0xb762df3c]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyObject_Call+0x5c)[0xb75ff1cc]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3cdd)[0xb76a722d]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x61a8)[0xb76a96f8]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x61a8)[0xb76a96f8]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x852)[0xb76ab5f2]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(+0x57e5a)[0xb762de5a]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyObject_Call+0x5c)[0xb75ff1cc]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(+0x3a165)[0xb7610165]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyObject_Call+0x5c)[0xb75ff1cc]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x54)[0xb76a2704]
/home/msnoise/anaconda/lib/libpython2.7.so.1.0(+0x10e8d2)[0xb76e48d2]
/lib/tls/i686/cmov/libpthread.so.0(+0x596e)[0xb75c296e]
/lib/tls/i686/cmov/libc.so.6(clone+0x5e)[0xb752898e]
======= Memory map: ========
00079000-0007a000 ---p 00000000 00:00 0
0007a000-0087a000 rw-p 00000000 00:00 0
0087a000-008a1000 r-xp 00000000 08:01 4087811 /home/msnoise/anaconda/lib/libm-2.5.so
008a1000-008a2000 r--p 00026000 08:01 4087811 /home/msnoise/anaconda/lib/libm-2.5.so
008a2000-008a3000 rw-p 00027000 08:01 4087811 /home/msnoise/anaconda/lib/libm-2.5.so
0103a000-0103b000 ---p 00000000 00:00 0
0103b000-0183b000 rw-p 00000000 00:00 0
0183b000-0183c000 ---p 00000000 00:00 0
0183c000-0203c000 rw-p 00000000 00:00 0
0203c000-0203d000 ---p 00000000 00:00 0
0203d000-0283d000 rw-p 00000000 00:00 0
0283d000-0283e000 ---p 00000000 00:00 0
0283e000-0303e000 rw-p 00000000 00:00 0
0303e000-0303f000 ---p 00000000 00:00 0
0303f000-0383f000 rw-p 00000000 00:00 0
0383f000-03840000 ---p 00000000 00:00 0
03840000-04040000 rw-p 00000000 00:00 0
04040000-04041000 ---p 00000000 00:00 0
04041000-04841000 rw-p 00000000 00:00 0
04841000-04842000 ---p 00000000 00:00 0
04842000-05042000 rw-p 00000000 00:00 0
05042000-05043000 ---p 00000000 00:00 0
05043000-05843000 rw-p 00000000 00:00 0
05843000-05844000 ---p 00000000 00:00 0
05844000-06044000 rw-p 00000000 00:00 0
06044000-06045000 ---p 00000000 00:00 0
06045000-06845000 rw-p 00000000 00:00 0
06845000-06846000 ---p 00000000 00:00 0
06846000-07046000 rw-p 00000000 00:00 0
07046000-07047000 ---p 00000000 00:00 0
07047000-07847000 rw-p 00000000 00:00 0
07847000-07848000 ---p 00000000 00:00 0
07848000-08048000 rw-p 00000000 00:00 0
08048000-08049000 r-xp 00000000 08:01 76972040 /home/msnoise/anaconda/bin/python2.7
08049000-0804a000 rw-p 00000000 08:01 76972040 /home/msnoise/anaconda/bin/python2.7
080b9000-09662000 rw-p 00000000 00:00 0 [heap]
09700000-097a3000 rw-p 00000000 00:00 0
097a3000-09800000 ---p 00000000 00:00 0
098f3000-098f4000 ---p 00000000 00:00 0
098f4000-0a0f4000 rw-p 00000000 00:00 0
0a0f4000-0a0f5000 ---p 00000000 00:00 0
0a0f5000-0a8f5000 rw-p 00000000 00:00 0
0a8f5000-0a8f6000 ---p 00000000 00:00 0
0a8f6000-0b0f6000 rw-p 00000000 00:00 0
0b0f6000-0b0f7000 ---p 00000000 00:00 0
0b0f7000-0b8f7000 rw-p 00000000 00:00 0
0b8f7000-0b8f8000 ---p 00000000 00:00 0
0b8f8000-0c0f8000 rw-p 00000000 00:00 0
0c0f8000-0c0f9000 ---p 00000000 00:00 0
0c0f9000-0c8f9000 rw-p 00000000 00:00 0
0c8f9000-0c8fa000 ---p 00000000 00:00 0
0c8fa000-0d0fa000 rw-p 00000000 00:00 0
0d0fa000-0d0fb000 ---p 00000000 00:00 0
0d0fb000-0d8fb000 rw-p 00000000 00:00 0
0d8fb000-0d8fc000 ---p 00000000 00:00 0
0d8fc000-0e0fc000 rw-p 00000000 00:00 0
0e0fc000-0e0fd000 ---p 00000000 00:00 0
0e0fd000-0e8fd000 rw-p 00000000 00:00 0
0e8fd000-0e8fe000 ---p 00000000 00:00 0
0e8fe000-0f0fe000 rw-p 00000000 00:00 0
0f0fe000-0f0ff000 ---p 00000000 00:00 0
0f0ff000-0f8ff000 rw-p 00000000 00:00 0
0f8ff000-0f900000 ---p 00000000 00:00 0
0f900000-10100000 rw-p 00000000 00:00 0
10100000-101ff000 rw-p 00000000 00:00 0
101ff000-10200000 ---p 00000000 00:00 0
10200000-102ff000 rw-p 00000000 00:00 0
102ff000-10300000 ---p 00000000 00:00 0
10300000-103ff000 rw-p 00000000 00:00 0
103ff000-10400000 ---p 00000000 00:00 0
104fe000-104ff000 ---p 00000000 00:00 0
104ff000-10cff000 rw-p 00000000 00:00 0
10cff000-10d00000 ---p 00000000 00:00 0 Aborted
________________________________________
From: msnoise-bounces(a)mailman-as.oma.be [msnoise-bounces(a)mailman-as.oma.be] on behalf of
Thomas Lecocq [thomas.lecocq(a)oma.be]
Sent: 23 October 2013 10:55
To: msnoise(a)mailman-as.oma.be
Subject: Re: [MSNoise] failed to run 01.scan_archive_threaded.py
with only 1 thread, to test?
thom
Le 23/10/2013 11:54, Wang, Xiao a écrit :
Please see the following output after I add up
"print source":
msnoise@seisapp:~/MSNoise-Temp/MSNoise-1.2$ python test.s01scan_archive.py init 4
2013-10-23 10:55:34,388 [INFO] *** Starting: Scan Archive ***
mtime: -1
init man!
will work on 4 threads
/home/msnoise/SDS/2010/3A/L002/HHE.D/3A.L002..HHE.D.2010.089
/home/msnoise/SDS/2010/3A/L002/HHE.D/3A.L002..HHE.D.2010.090
/home/msnoise/SDS/2010/3A/L002/HHE.D/3A.L002..HHE.D.2010.091
/home/msnoise/SDS/2010/3A/L002/HHE.D/3A.L002..HHE.D.2010.092
Traceback (most recent call last):
File "test.s01scan_archive.py", line 204, in <module>
t.start()
File "/home/msnoise/anaconda/lib/python2.7/threading.py", line 743, in
start
_start_new_thread(self.__bootstrap, ())
thread.error: can't start new thread
Error: msr_unpack_data((null)): Cannot allocate diff buffer
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot allocate diff buffer
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: msr_unpack(): Cannot allocate memory
Error: msr_init(): Cannot allocate memory
Error: msr_unpack_data((null)): Cannot (re)allocate memory
Error: seg_init(): Cannot allocate memory
Error: msr_init(): Cannot allocate memory
Segmentation fault
________________________________________
From: msnoise-bounces(a)mailman-as.oma.be [msnoise-bounces(a)mailman-as.oma.be] on behalf of
Thomas Lecocq [thomas.lecocq(a)oma.be]
Sent: 23 October 2013 10:48
To: msnoise(a)mailman-as.oma.be
Subject: Re: [MSNoise] failed to run 01.scan_archive_threaded.py
Xiao,
edit s01scan_archive.py and add this line
print source
before
data = read(source, quality=False)
that should be at Line72.
and send the output,
Thom
Le 23/10/2013 11:42, Wang, Xiao a écrit :
--
Dr. Thomas Lecocq
Geologist
Seismology - Gravimetry
Royal Observatory of Belgium
*
* * * * *
* * * *
---------
http://www.seismology.be
http://twitter.com/#!/Seismologie_be
_______________________________________________
MSNoise mailing list
MSNoise(a)mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise
In the SDS folder, there are only mseed files, no
other format files.
Xiao
-----Original Message-----
From: msnoise-bounces(a)mailman-as.oma.be [mailto:msnoise-bounces@mailman-as.oma.be] On
Behalf Of Thomas Lecocq
Sent: 23 October 2013 10:36
To: msnoise(a)mailman-as.oma.be
Subject: Re: [MSNoise] failed to run 01.scan_archive_threaded.py
Xiao,
Le 23/10/2013 11:29, Wang, Xiao a écrit :
--
Dr. Thomas Lecocq
Geologist
Seismology - Gravimetry
Royal Observatory of Belgium
*
* * * * *
* * * *
---------
http://www.seismology.be
http://twitter.com/#!/Seismologie_be
_______________________________________________
MSNoise mailing list
MSNoise(a)mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise
_______________________________________________
MSNoise mailing list
MSNoise(a)mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise I put my SDS data files in /home/msnoise/SDS
directory. In table config, I set value of data_folder is /home/msnoise/SDS, value of
data_structure is SDS, and value of export_format is MSEED.
This looks OK. Do you
have anything else than mseed files in the folders ?
Thomas
Xiao
________________________________________
From: msnoise-bounces(a)mailman-as.oma.be
[msnoise-bounces(a)mailman-as.oma.be] on behalf of Thomas Lecocq
[thomas.lecocq(a)oma.be]
Sent: 23 October 2013 10:24
To: msnoise(a)mailman-as.oma.be
Subject: Re: [MSNoise] failed to run 01.scan_archive_threaded.py
Xiao,
what is your data archive format and path ? (the configuration bits)
Thomas
Le 23/10/2013 11:23, Wang, Xiao a écrit :
--
Dr. Thomas Lecocq
Geologist
Seismology - Gravimetry
Royal Observatory of Belgium
*
* * * * *
* * * *
---------
http://www.seismology.be
http://twitter.com/#!/Seismologie_be
_______________________________________________
MSNoise mailing list
MSNoise(a)mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise
_______________________________________________
MSNoise mailing list
MSNoise(a)mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise Hi Thomas,
I try script python s01scan_archive.py init 4, but I still get same exception. I check
database and tables of jobs, filters and data_availability are empty.
Regards,
Xiao
Screenshot:
msnoise@seisapp:~/MSNoise-Temp/MSNoise-1.2$ python s01scan_archive.py
init 4
2013-10-23 10:21:32,796 [INFO] *** Starting: Scan Archive ***
mtime: -1
init man!
will work on 4 threads
2013-10-23 10:21:33,090 [DEBUG] 3A.L002..HHE.D.2010.089: Before
Start-Date! (0.25) Traceback (most recent call last):
File "s01scan_archive.py", line 203, in <module>
t.start()
File "/home/msnoise/anaconda/lib/python2.7/threading.py", line 743, in
start
_start_new_thread(self.__bootstrap, ())
thread.error: can't start new thread
2013-10-23 10:21:33,173 [DEBUG] 3A.L002..HHE.D.2010.090: Before
Start-Date! (0.33) Traceback (most recent call last):
File "_ctypes/callbacks.c", line 314, in 'calling callback
function'
File
"/home/msnoise/anaconda/lib/python2.7/site-packages/obspy-0.8.4-py2.7-linux-i686.egg/obspy/mseed/core.py",
line 261, in allocate_data
data = np.empty(samplecount, dtype=DATATYPES[sampletype])
MemoryError Segmentation fault
________________________________________
From: msnoise-bounces(a)mailman-as.oma.be
[msnoise-bounces(a)mailman-as.oma.be] on behalf of Thomas Lecocq
[thomas.lecocq(a)oma.be]
Sent: 23 October 2013 08:59
To: msnoise(a)mailman-as.oma.be
Subject: Re: [MSNoise] failed to run 01.scan_archive_threaded.py
Hello Xiao,
That is weird, could you test using more than 1 thread:
python s01scan_archive.py init 4
where 4 means 4 threads
Thomas
Le 22/10/2013 16:20, Wang, Xiao a écrit :
> Hi Thomas,
>
> I downloaded MSNoise 1.2 and passed s001configurator.py and
s002populate_station_table.py. But I encountered error when I call script python
s01scan_archive.py init.
>
> Any idea?
>
> Xiao
>
>
> The following is the screenshot:
>
> msnoise@seisapp:~/MSNoise-Temp/MSNoise-1.2$ python
> s001configurator.py Updating Config Table Updating Station Table
> Updating Filter Table Done !
>
> msnoise@seisapp:~/MSNoise-Temp/MSNoise-1.2$ python
> s002populate_station_table.py
>
>>> Populating the Station table
> Adding: 3A L002
> Adding: 3A L003
> Adding: 3A L004
> Adding: 3A L005
> Adding: 3A L006
> Adding: 3A L007
> Adding: 3A L008
> Adding: 3A L009
> Adding: 3A L101
> Adding: 3A L102
> Adding: 3A L103
> Adding: 3A L104
> Adding: 3A L105
> Adding: 3A L106
> Adding: 3A L107
> Adding: 3A L201
> Adding: 3A QC08
> Adding: 3A QC11
> Adding: 3A U16B
> Adding: 3A U40B
> Adding: 3A U69B
> Adding: 3A UO2B
>
> msnoise@seisapp:~/MSNoise-Temp/MSNoise-1.2$ python
> s01scan_archive.py init
> 2013-10-22 15:14:14,516 [INFO] *** Starting: Scan Archive ***
> mtime: -1
> init man!
> will work on 1 threads
> Traceback (most recent call last):
> File "s01scan_archive.py", line 203, in <module>
> t.start()
> File "/home/msnoise/anaconda/lib/python2.7/threading.py", line 743,
in start
> _start_new_thread(self.__bootstrap, ())
> thread.error: can't start new thread Traceback (most recent call
> last):
> File "_ctypes/callbacks.c", line 314, in 'calling callback
function'
> File
"/home/msnoise/anaconda/lib/python2.7/site-packages/obspy-0.8.4-py2.7-linux-i686.egg/obspy/mseed/core.py",
line 261, in allocate_data
> data = np.empty(samplecount, dtype=DATATYPES[sampletype])
> MemoryError Segmentation fault
>
>
>
>
>
>> Hi,
>>
>> Please donwload the latest MSNoise release, there are quite a
>> number of bugfix and improvements on the way memory and threads are handled !
>>
>> Let me know how it goes !
>>
>> Thomas
>>
>> ps : please subscribe to the list in order to have your messages
>> delivered automatically (this one went to "moderation")
> _______________________________________________
> MSNoise mailing list
> MSNoise(a)mailman-as.oma.be
> http://mailman-as.oma.be/mailman/listinfo/msnoise
--
Dr. Thomas Lecocq
Geologist
Seismology - Gravimetry
Royal Observatory of Belgium
*
* * * * *
* * * *
---------
http://www.seismology.be
http://twitter.com/#!/Seismologie_be
_______________________________________________
MSNoise mailing list
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http://mailman-as.oma.be/mailman/listinfo/msnoise
_______________________________________________
MSNoise mailing list
MSNoise(a)mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise
--
Dr. Thomas Lecocq
Geologist
Seismology - Gravimetry
Royal Observatory of Belgium
*
* * * * *
* * * *
---------
http://www.seismology.be
http://twitter.com/#!/Seismologie_be
_______________________________________________
MSNoise mailing list
MSNoise(a)mailman-as.oma.be
http://mailman-as.oma.be/mailman/listinfo/msnoise
_______________________________________________
MSNoise mailing list
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