Comments (5)
Which type of compiler are you using? I've encountered this error with Intel on certain machines, but it appears to be a compiler issue an not necessarily a code issue. The fix with the Intel compilers on one of my machines was accomplished by the addition of the compiler flag -heap-arrays 8192
where 8192 is the machine's stack size (ulimit -s
). This seems to clear up the issue because Intel does not automatically move implicitly created arrays to the heap, leading to a segfault. These implicit arrays are created inside the netCDF routines. The fix needed to be applied to both the netCDF Fortran library and the adcirc2netcdf.f90
code itself.
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I am using gfortran compiler , I tried compiling with intel but it gives me a error and I couldn't figure out yet.
here is the error
:~/Documents/KalpanaTesting_DONE/script/asgs/output$ make adcirc2netcdf compiler=intel MACHINENAME=poseidon NETCDF=enable NETCDF4=enable NETCDF4_COMPRESSION=enable
ifort -cpp -i-dynamic -DASGSNETCDF -DASGSNETCDF -DHAVE_NETCDF4 -DNETCDF_CAN_DEFLATE -I. -I/home/fhrl/Documents/Surge/scripts/netcdf/include -L/home/fhrl/Documents/Surge/scripts/netcdf/lib -c logging.f90 -lnetcdff
ifort: command line remark #10148: option '-i-dynamic' not supported
logging.f90(222): error #7013: This module file was not generated by any release of this compiler. [NETCDF]
use netcdf
----^
logging.f90(420): error #7013: This module file was not generated by any release of this compiler. [NETCDF]
use netcdf
----^
logging.f90(425): error #6404: This name does not have a type, and must have an explicit type. [NF90_NOERR]
if(ncstatus.ne.nf90_noerr)then
---------------^
logging.f90(426): error #6404: This name does not have a type, and must have an explicit type. [NF90_STRERROR]
write(,'(a,a)') "ERROR: ",trim(nf90_strerror(ncstatus))
-----------------------------------^
logging.f90(426): error #6362: The data types of the argument(s) are invalid. [TRIM]
write(,'(a,a)') "ERROR: ",trim(nf90_strerror(ncstatus))
-----------------------------------^
compilation aborted for logging.f90 (code 1)
makefile:170: recipe for target 'logging.mod' failed
make: *** [logging.mod] Error 1
from asgs.
Unfortunately, I'm not familiar enough with gfortran
to know if it has some of the same heap allocation issues as Intel, though I don't think it does. The error from your intel compile is because your netCDF library was compiled with gfortran. You may try to debug your original error using gdb
, which is the GNU debugger. It should give you some additional information that can help you see exactly where the code is going wrong. You should include -g -fbacktrace
when compiling both netCDF and adcirc2netcdf to generate debugging information that can be used by gdb
.
from asgs.
Thanks Zach
I will try to recompile fortran library with intel and will check if the problem persists
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Hello @ArslaanK I concur with @zcobell about the intel compile. On the issue of the segmentation fault, I think I found and fixed this a while back in the 2014stable branch. I just tried to reproduce this issue with some test files from the shinnecock inlet test problem, and everything went as expected. I will close this issue, but we can reopen it if things are still not running as expected for you.
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