I have built NumPy 1.1.0 on RedHat Enterprise 3 (Linux 2.4.21 with gcc 3.2.3 and glibc 2.3.2) and Python 2.5.1. When I run numpy.test() I get a core dump, as follows. I haven't noticed any special errors during the build. Should I post the entire terminal output from "python setup.py install"? Maybe as an attachment? Let me know if I can provide any more info. Thanks a lot, James. --- [iraf@sbfirf01 DRSetupScripts]$ python Python 2.5.1 (r251:54863, Jul 28 2008, 19:08:11) [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-20)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
import numpy numpy.test() Numpy is installed in /astro/iraf/i686/gempylocal/lib/python2.5/site-packages/numpy Numpy version 1.1.0 Python version 2.5.1 (r251:54863, Jul 28 2008, 19:08:11) [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-20)] Found 2/2 tests for numpy.core.tests.test_ufunc Found 143/143 tests for numpy.core.tests.test_regression Found 63/63 tests for numpy.core.tests.test_unicode Found 7/7 tests for numpy.core.tests.test_scalarmath Found 3/3 tests for numpy.core.tests.test_errstate Found 16/16 tests for numpy.core.tests.test_umath Found 12/12 tests for numpy.core.tests.test_records Found 70/70 tests for numpy.core.tests.test_numeric Found 18/18 tests for numpy.core.tests.test_defmatrix Found 36/36 tests for numpy.core.tests.test_numerictypes Found 286/286 tests for numpy.core.tests.test_multiarray Found 3/3 tests for numpy.core.tests.test_memmap Found 4/4 tests for numpy.distutils.tests.test_fcompiler_gnu Found 5/5 tests for numpy.distutils.tests.test_misc_util Found 2/2 tests for numpy.fft.tests.test_fftpack Found 3/3 tests for numpy.fft.tests.test_helper Found 15/15 tests for numpy.lib.tests.test_twodim_base Found 1/1 tests for numpy.lib.tests.test_regression Found 4/4 tests for numpy.lib.tests.test_polynomial Found 43/43 tests for numpy.lib.tests.test_type_check Found 1/1 tests for numpy.lib.tests.test_financial Found 1/1 tests for numpy.lib.tests.test_machar Found 53/53 tests for numpy.lib.tests.test_function_base Found 6/6 tests for numpy.lib.tests.test_index_tricks Found 15/15 tests for numpy.lib.tests.test_io Found 10/10 tests for numpy.lib.tests.test_arraysetops Found 1/1 tests for numpy.lib.tests.test_ufunclike Found 5/5 tests for numpy.lib.tests.test_getlimits Found 24/24 tests for numpy.lib.tests.test__datasource Found 49/49 tests for numpy.lib.tests.test_shape_base Found 3/3 tests for numpy.linalg.tests.test_regression Found 89/89 tests for numpy.linalg.tests.test_linalg Found 36/36 tests for numpy.ma.tests.test_old_ma Found 94/94 tests for numpy.ma.tests.test_core Found 15/15 tests for numpy.ma.tests.test_extras Found 17/17 tests for numpy.ma.tests.test_mrecords Found 4/4 tests for numpy.ma.tests.test_subclassing Found 7/7 tests for numpy.tests.test_random Found 16/16 tests for numpy.testing.tests.test_utils Found 5/5 tests for numpy.tests.test_ctypeslib ..................................................................................................................................................................................................................................................................................................Floating exception (core dumped)
On Tue, Jul 29, 2008 at 14:16, James Turner <jturner@gemini.edu> wrote:
I have built NumPy 1.1.0 on RedHat Enterprise 3 (Linux 2.4.21 with gcc 3.2.3 and glibc 2.3.2) and Python 2.5.1. When I run numpy.test() I get a core dump, as follows. I haven't noticed any special errors during the build. Should I post the entire terminal output from "python setup.py install"? Maybe as an attachment? Let me know if I can provide any more info.
Can you do numpy.test(verbosity=2) ? That will print out the name of the test before running it, so we will know exactly which test caused the core dump. A gdb backtrace would also help. -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco
I'm getting this too Ticket #652 ... ok Ticket 662.Segmentation fault Robert Kern wrote:
On Tue, Jul 29, 2008 at 14:16, James Turner <jturner@gemini.edu> wrote:
I have built NumPy 1.1.0 on RedHat Enterprise 3 (Linux 2.4.21 with gcc 3.2.3 and glibc 2.3.2) and Python 2.5.1. When I run numpy.test() I get a core dump, as follows. I haven't noticed any special errors during the build. Should I post the entire terminal output from "python setup.py install"? Maybe as an attachment? Let me know if I can provide any more info.
Can you do
numpy.test(verbosity=2)
? That will print out the name of the test before running it, so we will know exactly which test caused the core dump.
A gdb backtrace would also help.
I am using an ATLAS 64 bit lapack 3.9.1. My cpu (4 cpus) ------------------------------------------------- processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 23 model name : Intel(R) Xeon(R) CPU X5460 @ 3.16GHz stepping : 6 cpu MHz : 3158.790 cache size : 6144 KB physical id : 0 siblings : 4 core id : 0 cpu cores : 4 fpu : yes fpu_exception : yes cpuid level : 10 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall nx lm constant_tsc pni monitor ds_cpl vmx est tm2 cx16 xtpr lahf_lm bogomips : 6321.80 clflush size : 64 cache_alignment : 64 address sizes : 38 bits physical, 48 bits virtual power management: ----------------------------------------------------------- A system trace ends with futex(0xc600bb0, FUTEX_WAKE, 1) = 0 2655 write(2, ".", 1) = 1 2655 futex(0xc600bb0, FUTEX_WAKE, 1) = 0 2655 futex(0xc600bb0, FUTEX_WAKE, 1) = 0 2655 futex(0xc600bb0, FUTEX_WAKE, 1) = 0 2655 futex(0xc600bb0, FUTEX_WAKE, 1) = 0 2655 futex(0xc600bb0, FUTEX_WAKE, 1) = 0 2655 futex(0xc600bb0, FUTEX_WAKE, 1) = 0 2655 --- SIGSEGV (Segmentation fault) @ 0 (0) --- 2655 +++ killed by SIGSEGV +++ ---------------------------------------- I get no core file Robert Kern wrote:
On Tue, Jul 29, 2008 at 14:16, James Turner <jturner@gemini.edu> wrote:
I have built NumPy 1.1.0 on RedHat Enterprise 3 (Linux 2.4.21 with gcc 3.2.3 and glibc 2.3.2) and Python 2.5.1. When I run numpy.test() I get a core dump, as follows. I haven't noticed any special errors during the build. Should I post the entire terminal output from "python setup.py install"? Maybe as an attachment? Let me know if I can provide any more info.
Can you do
numpy.test(verbosity=2)
? That will print out the name of the test before running it, so we will know exactly which test caused the core dump.
A gdb backtrace would also help.
On Tue, Jul 29, 2008 at 1:16 PM, James Turner <jturner@gemini.edu> wrote:
I have built NumPy 1.1.0 on RedHat Enterprise 3 (Linux 2.4.21 with gcc 3.2.3 and glibc 2.3.2) and Python 2.5.1. When I run numpy.test() I get a core dump, as follows. I haven't noticed any special errors during the build. Should I post the entire terminal output from "python setup.py install"? Maybe as an attachment? Let me know if I can provide any more info.
Thanks a lot,
James.
---
[iraf@sbfirf01 DRSetupScripts]$ python Python 2.5.1 (r251:54863, Jul 28 2008, 19:08:11) [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-20)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
import numpy numpy.test() Numpy is installed in /astro/iraf/i686/gempylocal/lib/python2.5/site-packages/numpy Numpy version 1.1.0 Python version 2.5.1 (r251:54863, Jul 28 2008, 19:08:11) [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-20)] Found 2/2 tests for numpy.core.tests.test_ufunc Found 143/143 tests for numpy.core.tests.test_regression Found 63/63 tests for numpy.core.tests.test_unicode Found 7/7 tests for numpy.core.tests.test_scalarmath Found 3/3 tests for numpy.core.tests.test_errstate Found 16/16 tests for numpy.core.tests.test_umath Found 12/12 tests for numpy.core.tests.test_records Found 70/70 tests for numpy.core.tests.test_numeric Found 18/18 tests for numpy.core.tests.test_defmatrix Found 36/36 tests for numpy.core.tests.test_numerictypes Found 286/286 tests for numpy.core.tests.test_multiarray Found 3/3 tests for numpy.core.tests.test_memmap Found 4/4 tests for numpy.distutils.tests.test_fcompiler_gnu Found 5/5 tests for numpy.distutils.tests.test_misc_util Found 2/2 tests for numpy.fft.tests.test_fftpack Found 3/3 tests for numpy.fft.tests.test_helper Found 15/15 tests for numpy.lib.tests.test_twodim_base Found 1/1 tests for numpy.lib.tests.test_regression Found 4/4 tests for numpy.lib.tests.test_polynomial Found 43/43 tests for numpy.lib.tests.test_type_check Found 1/1 tests for numpy.lib.tests.test_financial Found 1/1 tests for numpy.lib.tests.test_machar Found 53/53 tests for numpy.lib.tests.test_function_base Found 6/6 tests for numpy.lib.tests.test_index_tricks Found 15/15 tests for numpy.lib.tests.test_io Found 10/10 tests for numpy.lib.tests.test_arraysetops Found 1/1 tests for numpy.lib.tests.test_ufunclike Found 5/5 tests for numpy.lib.tests.test_getlimits Found 24/24 tests for numpy.lib.tests.test__datasource Found 49/49 tests for numpy.lib.tests.test_shape_base Found 3/3 tests for numpy.linalg.tests.test_regression Found 89/89 tests for numpy.linalg.tests.test_linalg Found 36/36 tests for numpy.ma.tests.test_old_ma Found 94/94 tests for numpy.ma.tests.test_core Found 15/15 tests for numpy.ma.tests.test_extras Found 17/17 tests for numpy.ma.tests.test_mrecords Found 4/4 tests for numpy.ma.tests.test_subclassing Found 7/7 tests for numpy.tests.test_random Found 16/16 tests for numpy.testing.tests.test_utils Found 5/5 tests for numpy.tests.test_ctypeslib
..................................................................................................................................................................................................................................................................................................Floating exception (core dumped)
Are you using ATLAS? If so, where did you get it and what cpu do you have? Chuck
Are you using ATLAS? If so, where did you get it and what cpu do you have?
Yes. I have Atlas 3.8.2. I think I got it from http://math-atlas.sourceforge.net. I also included Lapack 3.1.1 from Netlib when building it from source. This worked on another machine. According to /proc/cpuinfo, I have a quad-processor (or core?) Intel Xeon. It is running the Linux 2.4 kernel (I needed to build a load of software including NumPy with an older glibc so it will run on older client machines). Maybe I shouldn't use ATLAS for a server installation, since it won't be tuned well? We're trying to keep things uniform across our sites though. Thanks! James.
my set up is similar. Same cpu's. Except I am using atlas 3.9.1 and gcc 4.2.4 James Turner wrote:
Are you using ATLAS? If so, where did you get it and what cpu do you have?
Yes. I have Atlas 3.8.2. I think I got it from http://math-atlas.sourceforge.net. I also included Lapack 3.1.1 from Netlib when building it from source. This worked on another machine.
According to /proc/cpuinfo, I have a quad-processor (or core?) Intel Xeon. It is running the Linux 2.4 kernel (I needed to build a load of software including NumPy with an older glibc so it will run on older client machines). Maybe I shouldn't use ATLAS for a server installation, since it won't be tuned well? We're trying to keep things uniform across our sites though.
Thanks!
James.
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Thanks everyone. I think I might try using the Netlib BLAS, since it's a server installation... but please let me know if you'd like me to troubleshoot this some more (the sooner the easier). James.
more info when /linalg.py(872)eigh() calls dsyevd I crash James Turner wrote:
Thanks everyone. I think I might try using the Netlib BLAS, since it's a server installation... but please let me know if you'd like me to troubleshoot this some more (the sooner the easier).
James.
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On Tue, Jul 29, 2008 at 2:48 PM, James Turner <jturner@gemini.edu> wrote:
Thanks everyone. I think I might try using the Netlib BLAS, since it's a server installation... but please let me know if you'd like me to troubleshoot this some more (the sooner the easier).
This smells like an ATLAS problem. You should seed a note to Clint Whaley (the ATLAS guy). IIRC, ATLAS has some hand coded asm routines and it seems that support for these very new processors might be broken. Chuck
Charles R Harris wrote:
This smells like an ATLAS problem.
I don't think so. I crash in a call to dsyevd which part of lapack but not atlas. Also, when I commented out the call to test_eigh_build I get zillions of errors like (look at the second one, warnings wasn't imported?) ====================================================================== ERROR: check_single (numpy.linalg.tests.test_linalg.TestSVD) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/ossetest/lib/python2.5/site-packages/numpy/linalg/tests/test_linalg.py", line 30, in check_single self.do(a, b) File "/home/ossetest/lib/python2.5/site-packages/numpy/linalg/tests/test_linalg.py", line 100, in do u, s, vt = linalg.svd(a, 0) File "/home/ossetest/lib/python2.5/site-packages/numpy/linalg/linalg.py", line 980, in svd s = s.astype(_realType(result_t)) ValueError: On entry to DLASD0 parameter number 9 had an illegal value ====================================================================== ERROR: Tests polyfit ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/ossetest/lib/python2.5/site-packages/numpy/ma/tests/test_extras.py", line 365, in test_polyfit assert_almost_equal(polyfit(x,y,3),numpy.polyfit(x,y,3)) File "/home/ossetest/lib/python2.5/site-packages/numpy/ma/extras.py", line 882, in polyfit warnings.warn("Polyfit may be poorly conditioned", np.RankWarning) NameError: global name 'warnings' is not defined
You should seed a note to Clint Whaley (the ATLAS guy). IIRC, ATLAS has some hand coded asm routines and it seems that support for these very new processors might be broken.
Chuck
------------------------------------------------------------------------
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oops. It is ATLAS. I was able to run with a nonoptimized lapack. Mathew Yeates wrote:
Charles R Harris wrote:
This smells like an ATLAS problem.
I don't think so. I crash in a call to dsyevd which part of lapack but not atlas. Also, when I commented out the call to test_eigh_build I get zillions of errors like (look at the second one, warnings wasn't imported?) ====================================================================== ERROR: check_single (numpy.linalg.tests.test_linalg.TestSVD) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/ossetest/lib/python2.5/site-packages/numpy/linalg/tests/test_linalg.py", line 30, in check_single self.do(a, b) File "/home/ossetest/lib/python2.5/site-packages/numpy/linalg/tests/test_linalg.py", line 100, in do u, s, vt = linalg.svd(a, 0) File "/home/ossetest/lib/python2.5/site-packages/numpy/linalg/linalg.py", line 980, in svd s = s.astype(_realType(result_t)) ValueError: On entry to DLASD0 parameter number 9 had an illegal value
====================================================================== ERROR: Tests polyfit ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/ossetest/lib/python2.5/site-packages/numpy/ma/tests/test_extras.py", line 365, in test_polyfit assert_almost_equal(polyfit(x,y,3),numpy.polyfit(x,y,3)) File "/home/ossetest/lib/python2.5/site-packages/numpy/ma/extras.py", line 882, in polyfit warnings.warn("Polyfit may be poorly conditioned", np.RankWarning) NameError: global name 'warnings' is not defined
You should seed a note to Clint Whaley (the ATLAS guy). IIRC, ATLAS has some hand coded asm routines and it seems that support for these very new processors might be broken.
Chuck
------------------------------------------------------------------------
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On Tue, Jul 29, 2008 at 17:41, Mathew Yeates <myeates@jpl.nasa.gov> wrote:
Charles R Harris wrote:
This smells like an ATLAS problem.
I don't think so. I crash in a call to dsyevd which part of lapack but not atlas. Also, when I commented out the call to test_eigh_build I get zillions of errors like (look at the second one, warnings wasn't imported?)
Fixed in SVN. -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco
What got fixed? Robert Kern wrote:
On Tue, Jul 29, 2008 at 17:41, Mathew Yeates <myeates@jpl.nasa.gov> wrote:
Charles R Harris wrote:
This smells like an ATLAS problem.
I don't think so. I crash in a call to dsyevd which part of lapack but not atlas. Also, when I commented out the call to test_eigh_build I get zillions of errors like (look at the second one, warnings wasn't imported?)
Fixed in SVN.
On Tue, Jul 29, 2008 at 18:00, Mathew Yeates <myeates@jpl.nasa.gov> wrote:
What got fixed?
(look at the second one, warnings wasn't imported?)
-- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco
This smells like an ATLAS problem. You should seed a note to Clint Whaley (the ATLAS guy). IIRC, ATLAS has some hand coded asm routines and it seems that support for these very new processors might be broken.
I believe the machine is a couple of years old, though it's a fairly high-end workstation. Anyway, I have submitted an ATLAS support request so they're aware of it: https://sourceforge.net/tracker/index.php?func=detail&aid=2032011&group_id=23725&atid=379483 Cheers, James.
Thanks, Robert.
Can you do
numpy.test(verbosity=2)
OK. Here is the line that fails: check_matvec (numpy.core.tests.test_numeric.TestDot)Floating exception (core dumped)
A gdb backtrace would also help.
OK. I'm pretty ignorant about using debuggers, but I did "gdb python core.23696" and got the following. Does that help? Thanks, James. --- GNU gdb Red Hat Linux (5.3.90-0.20030710.40rh) Copyright 2003 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details. This GDB was configured as "i386-redhat-linux-gnu"...Using host libthread_db library "/lib/tls/libthread_db.so.1". Core was generated by `python numpytest.py'. Program terminated with signal 8, Arithmetic exception. Reading symbols from /lib/tls/libpthread.so.0...done. Loaded symbols for /lib/tls/libpthread.so.0 Reading symbols from /lib/libdl.so.2...done. Loaded symbols for /lib/libdl.so.2 Reading symbols from /lib/libutil.so.1...done. Loaded symbols for /lib/libutil.so.1 Reading symbols from /lib/tls/libm.so.6...done. Loaded symbols for /lib/tls/libm.so.6 Reading symbols from /lib/tls/libc.so.6...done. Loaded symbols for /lib/tls/libc.so.6 Reading symbols from /lib/ld-linux.so.2...done. Loaded symbols for /lib/ld-linux.so.2 Reading symbols from /astro/iraf/i686/gempylocal/lib/python2.5/site-packages/numpy/core/multiarray.so...done. Loaded symbols for /astro/iraf/i686/gempylocal/lib/python2.5/site-packages/numpy/core/multiarray.so Reading symbols from /astro/iraf/i686/gempylocal/lib/python2.5/site-packages/numpy/core/umath.so...done. Loaded symbols for /astro/iraf/i686/gempylocal/lib/python2.5/site-packages/numpy/core/umath.so Reading symbols from /astro/iraf/i686/gempylocal/lib/python2.5/lib-dynload/strop.so...done. Loaded symbols for /astro/iraf/i686/gempylocal/lib/python2.5/lib-dynload/strop.so Reading symbols from /astro/iraf/i686/gempylocal/lib/python2.5/site-packages/numpy/core/_sort.so...done. 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participants (5)
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Charles R Harris -
David Cournapeau -
James Turner -
Mathew Yeates -
Robert Kern