Hi Scott,
Thanks ... I will double check about this with the support crew at the
site then ...
Best,
Vlad
On 2020-10-20 04:10, Scott Brozell wrote:
> Hi again,
>
> That bit about "on a supercomputer" didn't penetrate my noggin
> initially. Go ahead call me Fickian (the 'F' can be pronounced
> with a 'Th' sound as well :).
>
> Anyway, this now seems like a not-so-super-computer issue. Ie,
> support there should verify their Intel and GNU compatibility.
> Here's some context:
>
> Intel compilers use the GNU tools on the cluster: header files, libraries, and
> linker. The details of Intel and GNU compatibility and interoperability can be
> controlled in several ways. On Foo clusters the default mechanism of control is
> based on modules. An alternative way to control compatibility and
> interoperability is with Intel compiler options; see the 'GNU gcc
> Interoperability' section of the Intel compiler man pages for details.
>
> To view the GNU compatibility, use the '-v' intel compiler option.
>
> scott
>
> On Mon, Oct 19, 2020 at 09:44:09PM -0400, Scott Brozell wrote:
>> On Mon, Oct 19, 2020 at 07:47:43PM +0200, Vlad Cojocaru wrote:
>>> I am trying to install Amber 20 on a supercomputer with the intel 19.1.1
>>> compiler but the serial compilation fails at cpptraj with the error below.
>>> Has anyone seen this before and has an idea how to fix it ?
>>>
>>> In file included from Traj_GmxXtc.cpp(1):
>>> Traj_GmxXtc.h(40): error: identifier "off_t" is undefined
>>> ?????????? std::vector<off_t> frameOffsets_; ///< Frame offsets for reading
>>> ?????????????????????????????????? ^
>>>
>>> compilation aborted for Traj_GmxXtc.cpp (code 2)
>>> ../config.h:45: recipe for target 'Traj_GmxXtc.o' failed
>>> make[4]: *** [Traj_GmxXtc.o] Error 2
>> I routinely build with intel; last was 19.0.5 on oct 15 on
>> Red Hat Enterprise Linux Server release 7.7 (Maipo)
>>
>> I don't have 19.1.1 but i suspect your problem is GNU/OS related.
>> off_t comes from sys/types.h via bits/types.h
>> My system has several versions of these but they haven't changed significantly:
>> 8 -rw-r--r-- 1 root root 6771 Apr 30 2019 /usr/include/sys/types.h
>> 8 -rw-r--r-- 1 root root 6838 Jan 24 2014 /usr/lib/x86_64-redhat-linux6E/include/sys/types.h
>> 8 -rw-r--r-- 1 root root 7729 Apr 30 2019 /usr/include/bits/types.h
>> 8 -rw-r--r-- 1 root root 7601 Jan 24 2014 /usr/lib/x86_64-redhat-linux6E/include/bits/types.h
>>
>> My first guess is that you have intel compilers layered on top of
>> really old gnu compilers.
>> So check into updating your gnu with your OS's package management tool.
>> If you send verbose and verbatim details then someone can probably quote
>> exactly what to execute. Those details should include
>> cat /etc/*release
>> gcc -v
>> icc -v
>>
>> For the compilers, eg, ...
>> gcc version 8.4.0 (GCC)
>> icc version 19.0.5.281 (gcc version 8.4.0 compatibility)
>>
>> scott
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=04%7C01%7Csbrozell%40iqb.rutgers.edu%7C3a2948c7fee247fe398608d87499bd0d%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637387550939775704%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=1w%2BpkIVffD8f468e5o8aB%2F7u8bt1yByxqjl%2BSPKeBx4%3D&reserved=0
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 20 2020 - 05:00:02 PDT
