I am working on the cluster that is available at my research institute, so I don't actually have root access. It is CentOS 8.3.2011 with openHPC. With the weird stl header file issues, it seemed that the compiler module had not been properly loaded, and then when I did properly load it, I didn't start a fresh configuration, and so the problems persisted. Now that I have done that the issues with math.h are solved.
However, trilinos is loaded as a module, and even with the fresh configuration it is unable to find the header. Even with //Path to a file. SACADO_CONFIG_H:FILEPATH=/opt/ohpc/pub/libs/gnu9/mpich/trilinos/13.0.0/include/Sacado.hpp //Path to a file. SACADO_TRAD_HPP:FILEPATH=/opt/ohpc/pub/libs/gnu9/mpich/trilinos/13.0.0/include/Sacado_trad.hpp in the CMakeCache.txt, and rerunning cmake, it is still unable to actually Sacado.hpp while compiling. I am also trying to contact the cluster administrators to double check they have installed trilinos correctly, but I still find it odd that even specifying the exact location of the headers in the cmake configuration still does not results in a successful compilation. On Thursday, May 27, 2021 at 5:53:48 a.m. UTC+2 Wolfgang Bangerth wrote: > On 5/26/21 11:17 AM, Alex Cumberworth wrote: > > It seems that the issues stem from not setting the include directories > > properly. Even with CPATH, C_INCLUDE_PATH, and CPLUS_INCLUDE_PATH set as > I > > mentioned in my previous response, I am running into errors. The > compilation > > proceeds for a while, but then at some point when cmath is included, it > fails > > to find math.h, > > > > [ 42%] Building CXX object > > source/sundials/CMakeFiles/obj_sundials_release.dir/arkode.cc.o > > > > In file included from > > > /home/ipausers/cumberworth/src/dealii-9.2.0/include/deal.II/base/numbers.h:28, > > from > > > /home/ipausers/cumberworth/src/dealii-9.2.0/build/include/deal.II/base/config.h:449, > > from > > /home/ipausers/cumberworth/src/dealii-9.2.0/source/sundials/arkode.cc:17: > > /opt/ohpc/pub/compiler/gcc/9.3.0/include/c++/9.3.0/cmath:45:15: fatal > error: > > math.h: No such file or directory > > 45 | #include_next <math.h> > > | ^~~~~~~~ > > compilation terminated. > > > > If I use make VERBOSE=1, I can manually modify the command to include > > > > -isystem /opt/ohpc/pub/compiler/gcc/9.3.0/include/c++/9.3.0 > > > > which solves that issue, but I don't know how to add this during > > configuration. > > I suspect that you will get an endless sequence of problems beyond just > this > one if you go down the road of trying to address this with compiler flags. > I > suspect that what is happening is that you compiled and installed GCC 9.3 > yourself, and then moved everything from the directory you installed it in > to > /opt/ohpc/pub/compiler/gcc/9.3.0? You will have to install GCC in a way so > that it knows where not only its header files are, but also the libraries, > the > linker, etc. > > What happens if you use that compiler (without passing extra flags) to > compile > a trivial .cc file that only #includes <cmath>? > > Best > W. > > -- > ------------------------------------------------------------------------ > Wolfgang Bangerth email: bang...@colostate.edu > www: http://www.math.colostate.edu/~bangerth/ > > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/3fb19862-5d00-4ad2-9bc7-eb065bcc19b8n%40googlegroups.com.
