Hi,
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 - 19:00:02 PDT
