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
>
>
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Received on Mon Oct 19 2020 - 19:30:02 PDT
