Re: [easybuild] Falcon --- Memory address map error --- Sanity check

[Lars Viklund]

"Good" news!

I managed to reproduce this on a Skylake Xeon machine in a container 
with CentOS 7.6.

https://gist.github.com/zao/95148a6da079fa8ea6fd9433c478d5d3

I don't have any solution yet, but at least it's not your particular 
environment that triggers the problem.

// Lars

On 2/13/20 12:19 PM, Ricardo Gregorio wrote:
Hi Lars,

Thanks for replying....

We are trying to build on...

CentOS 7.5
Intel Gold (skylake)


Regards,
Ricardo Gregorio
Research and Systems Administrator


-----Original Message-----
From: easybuild-requ...@lists.ugent.be <easybuild-requ...@lists.ugent.be> On 
Behalf Of Lars Viklund
Sent: 12 February 2020 17:59
To: easybuild@lists.ugent.be
Subject: Re: [easybuild] Falcon --- Memory address map error --- Sanity check

Hi!

I gave that easyconfig a try on a few different machines and can't seem to get 
it to misbehave like you demonstrate.

They were:

* Ubuntu 18.04, 8700K
* Ubuntu 16.04, Broadwell,
* CentOS 7.6 (container on 8700K).

Could you please let us know what OS release and processor are you building 
this on?

With kind regards,
Lars Viklund, HPC2N

On 2/12/20 11:54 AM, ricardo.grego...@rothamsted.ac.uk wrote:
Hi all

Hope someone has come across this before and can assist...

we are trying to build Falcon-1.8.8-intel-2017b.eb
[https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Feasybuilders%2Feasybuild-easyconfigs%2Fblob%2Fmaster%2Feasybuild%2Feasyconfigs%2Ff%2FFALCON%2FFALCON-1.8.8-intel-2017b.eb&amp;data=01%7C01%7Cricardo.gregorio%40rothamsted.ac.uk%7C358869c04b624531b9bf08d7afe57053%7Cb688362589414342b0e37b8cc8392f64%7C1&amp;sdata=PDavRg3wx16PUo0xI%2B1tqHz7OUqaJyqVURNcmCp2dN0%3D&amp;reserved=0].
However it is failing during the sanity check stage and throwing some
Memory address mapping errors

+++++++++++++++++++++++
Extract of error message
+++++++++++++++++++++++

*** Error in `/.../eb/software/Python/2.7.14-intel-2017b/bin/python':
double free or corruption (out): 0x0000000000c3c510 *** =======
Backtrace: ========= /usr/lib64/libc.so.6(+0x81499)[0x2ad5c6c56499]
/.../eb/software/FALCON/1.8.8-intel-2017b/lib/python2.7/site-packages/
falcon_kit-0.7-py2.7-linux-x86_64.egg/ext_falcon.so(find_best_aln_rang
e+0xb14)
[0x2ad5d3f3e294]
/.../eb/software/FALCON/1.8.8-intel-2017b/lib/python2.7/site-packages/
falcon_kit-0.7-py2.7-linux-x86_64.egg/ext_falcon.so(generate_consensus
+0x1bd)
[0x2ad5d3f3f01d]
/.../eb/software/Python/2.7.14-intel-2017b/lib/python2.7/lib-dynload/
_ctypes.so(ffi_call_unix64+0x4c)[0x2ad5d3d2881c]
/.../eb/software/Python/2.7.14-intel-2017b/lib/python2.7/lib-dynload/
_ctypes.so(ffi_call+0x579)[0x2ad5d3d27b29]
/.../eb/software/Python/2.7.14-intel-2017b/lib/python2.7/lib-dynload/
_ctypes.so(_ctypes_callproc+0x5ef)[0x2ad5d3d1d5cf]
/.../eb/software/Python/2.7.14-intel-2017b/lib/python2.7/lib-dynload/
_ctypes.so(+0xd926)[0x2ad5d3d17926]
/.../eb/software/Python/2.7.14-intel-2017b/lib/libpython2.7.so.
1.0(PyObject_Call+0x5a)[0x2ad5c5a37eba]
...
/usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2ad5c6bf7445]



/.../eb/software/Python/2.7.14-intel-2017b/bin/python[0x4012e9]
======= Memory map: ========
00400000-00418000 r-xp 00000000 00:28 9014510081                         /.../
eb/software/Python/2.7.14-intel-2017b/bin/python2.7
00618000-00619000 r--p 00018000 00:28 9014510081                         /.../
eb/software/Python/2.7.14-intel-2017b/bin/python2.7
00619000-0061a000 rw-p 00019000 00:28 9014510081                         /.../
eb/software/Python/2.7.14-intel-2017b/bin/python2.7
009d7000-00ee7000 rw-p 00000000 00:00 0 [heap]
2ad5c57a8000-2ad5c57ca000 r-xp 00000000 fd:00 790170                     /usr/
lib64/ld-2.17.so
2ad5c57ca000-2ad5c57cc000 rw-p 00000000 00:00 0
2ad5c57cc000-2ad5c57dd000 r-xp 00000000 00:28 7731022159                 /.../
eb/software/bzip2/1.0.6-GCCcore-6.4.0/lib/libbz2.so.1.0.6
2ad5c57dd000-2ad5c57de000 r--p 00010000 00:28 7731022159                 /.../
eb/software/bzip2/1.0.6-GCCcore-6.4.0/lib/libbz2.so.1.0.6
2ad5c57de000-2ad5c57df000 rw-p 00011000 00:28 7731022159                 /.../
eb/software/bzip2/1.0.6-GCCcore-6.4.0/lib/libbz2.so.1.0.6
2ad5c57df000-2ad5c57e0000 rwxp 00000000 00:00 0
2ad5c57e0000-2ad5c57e3000 rw-p 00000000 00:00 0
2ad5c57e3000-2ad5c57f9000 r-xp 00000000 00:28 7730996980                 /.../
eb/software/GCCcore/6.4.0/lib64/libgcc_s.so.1
2ad5c57f9000-2ad5c57fa000 r--p 00015000 00:28 7730996980                 /.../
eb/software/GCCcore/6.4.0/lib64/libgcc_s.so.1
2ad5c57fa000-2ad5c57fb000 rw-p 00016000 00:28 7730996980                 /.../
eb/software/GCCcore/6.4.0/lib64/libgcc_s.so.1
2ad5c57fb000-2ad5c58c1000 rw-p 00000000 00:00 0
2ad5c58f1000-2ad5c59b1000 rw-p 00000000 00:00 0
2ad5c59b1000-2ad5c59c7000 r-xp 00000000 00:28 7730852699                 /.../
eb/software/zlib/1.2.11-GCCcore-6.4.0/lib/libz.so.1.2.11
2ad5c59c7000-2ad5c59c8000 r--p 00015000 00:28 7730852699                 /.../
eb/software/zlib/1.2.11-GCCcore-6.4.0/lib/libz.so.1.2.11
2ad5c59c8000-2ad5c59c9000 rw-p 00016000 00:28 7730852699                 /.../
eb/software/zlib/1.2.11-GCCcore-6.4.0/lib/libz.so.1.2.11
2ad5c59c9000-2ad5c59ca000 r--p 00021000 fd:00 790170                     /usr/
lib64/ld-2.17.so
2ad5c59ca000-2ad5c59cb000 rw-p 00022000 fd:00 790170                     /usr/
lib64/ld-2.17.so
...
2ad5d47ae000-2ad5d486f000 rw-p 00000000 00:00 0
2ad5d8000000-2ad5d8021000 rw-p 00000000 00:00 0
2ad5d8021000-2ad5dc000000 ---p 00000000 00:00 0
7ffdeefc9000-7ffdeefef000 rw-p 00000000 00:00 0 [stack]
7ffdeeff5000-7ffdeeff7000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
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