Lars, Excellent and thanks a lot for taking your time to look into this...
I will give it a try early next week and report back.... Assist was much appreciated 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.
