Hi Ricardo,
The easyconfig I made for this can be found in a pull request against
the easybuild-easyconfigs repository at
https://github.com/easybuilders/easybuild-easyconfigs/pull/9873
They are targetting the 2019b toolchain and as such have a dependency on
a slightly more recent Python version. As the Python module now has
scipy and numpy separated into the SciPy-bundle module, I've included an
easyconfig for that as well.
You can give your EasyBuild "--from-pr=9873" to get the easyconfigs from
the PR.
// Lars
On 2/17/20 12:56 PM, Ricardo Gregorio wrote:
Hi Lars,
Would you mind sharing the steps you have done to successfully build Falcon, as
I am still having issues????
I have made a copy of FALCON-1.8.8-intel-2017b.eb and try to build as follows:
$ eb --optarch=march=skylake-avx512 --job-cores=8 FALCON-1.8.8-intel-2019b.eb
--try-toolchain=intel,2019b -r
Regards,
Ricardo Gregorio
Research and Systems Administrator
-----Original Message-----
From: [email protected] <[email protected]> On
Behalf Of Lars Viklund
Sent: 13 February 2020 20:21
To: [email protected]
Subject: Re: [easybuild] Falcon --- Memory address map error --- Sanity check
I made a copy of the easyconfig and built with intel/2019b instead.
Having done so, the sanity checks are passing. This doesn't necessarily mean
that the actual software works, but it's probably better, assuming you have a
license for the Intel compilers in 2019b.
// Lars
On 2020-02-13 18:23, Lars Viklund wrote:
"Good" news!
I managed to reproduce this on a Skylake Xeon machine in a container
with CentOS 7.6.
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgist
.github.com%2Fzao%2F95148a6da079fa8ea6fd9433c478d5d3&data=01%7C01%
7Cricardo.gregorio%40rothamsted.ac.uk%7C99d4775a1ac64eaeb34008d7b0c267
7d%7Cb688362589414342b0e37b8cc8392f64%7C1&sdata=xerczbh9rvOCc8Csyk
kk%2Bld3L6iV9Wtty5Oo%2FpkuAS4%3D&reserved=0
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: [email protected]
<[email protected]> On Behalf Of Lars Viklund
Sent: 12 February 2020 17:59
To: [email protected]
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, [email protected] 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&data=01%7C01%7Cricardo.gregorio%40rothamsted.ac.uk%7C99d4775a1ac64eaeb34008d7b0c2677d%7Cb688362589414342b0e37b8cc8392f64%7C1&sdata=PE6JcZA1ePrhvW2zu2RAEE0z3UUhS4ty3lWvHHnBJFM%3D&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-package
s/
falcon_kit-0.7-py2.7-linux-x86_64.egg/ext_falcon.so(find_best_aln_ra
ng
e+0xb14)
[0x2ad5d3f3e294]
/.../eb/software/FALCON/1.8.8-intel-2017b/lib/python2.7/site-package
s/
falcon_kit-0.7-py2.7-linux-x86_64.egg/ext_falcon.so(generate_consens
us
+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]
Rothamsted Research is a company limited by guarantee, registered in
England at Harpenden, Hertfordshire, AL5 2JQ under the registration
number 2393175 and a not for profit charity number 802038.
Rothamsted Research is a company limited by guarantee, registered in England at
Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a
not for profit charity number 802038.
