"make clean; make stencil=iso3dfd" error

[mengshanfeng]

"make clean; make stencil=iso3dfd" error

[chuckyount]

@mengshanfeng: Unfortunately, I can't figure out from your output what the actual error is. Maybe the error message was cut out of the output. Can you capture all the stdout and stderr, put that in something like https://pastebin.com/ and put a link to it here? Thanks.

[mengshanfeng]

https://pastebin.com/nEt579kS
@chuckyount
https://pastebin.com/nEt579kS
i paste the whole message here and Many thanks!

[chuckyount]

This seems very odd indeed. The file /yask-master/build/kernel/yask_kernel.iso3dfd.avx2/gen/yask_stencil_code.hpp is created and then successfully used by a number of scripts. But then the compiler fails with the message
/yask-master/src/kernel/lib/yask_stencil.hpp(38): catastrophic error: cannot open source file "/yask-master/build/kernel/yask_kernel.iso3dfd.avx2/gen/yask_stencil_code.hpp". It looks like the file disappeared or is somehow unreadable by the compiler.

Assuming you haven't changed anything, can you run gcc -v; mpiicc -v; ls -l /yask-master/build/kernel/yask_kernel.iso3dfd.avx2/gen and paste the results?

[mengshanfeng]

@chuckyount Hi,
$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.4.0-1ubuntu118.04.1' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 7.4.0 (Ubuntu 7.4.0-1ubuntu118.04.1)

$ mpiicc -v
mpiicc for the Intel(R) MPI Library 2019 Update 3 for Linux*
Copyright 2003-2019, Intel Corporation.
icc version 19.0.3.199 (gcc version 7.4.0 compatibility)

$ ls -l /yask-master/build/kernel/yask_kernel.iso3dfd.avx2/gen
total 228
-rwxrwxrwx 1 5335 Dec 4 16:39 yask_block_loops.hpp
-rwxrwxrwx 1 9127 Dec 4 16:39 yask_layout_macros.hpp
-rwxrwxrwx 1 26232 Dec 4 16:39 yask_layouts.hpp
-rwxrwxrwx 1 5014 Dec 4 16:39 yask_mini_block_loops.hpp
-rwxrwxrwx 1 4912 Dec 4 16:39 yask_misc_loops.hpp
-rwxrwxrwx 1 4826 Dec 4 16:39 yask_rank_loops.hpp
-rwxrwxrwx 1 5125 Dec 4 16:39 yask_region_loops.hpp
-rwxrwxrwx 1 142428 Dec 4 16:39 yask_stencil_code.hpp
-rwxrwxrwx 1 3746 Dec 4 16:39 yask_sub_block_loops.hpp
-rwxrwxrwx 1 942 Dec 4 16:39 yask_var_code.hpp

[chuckyount]

I just can't figure out what's going on. The file "/yask-master/build/kernel/yask_kernel.iso3dfd.avx2/gen/yask_stencil_code.hpp" exists and has ample read permissions according to your output above, but the compiler error says it cannot open this file. As far as I know, nobody else has had this issue. We need to figure out why the compiler cannot open the file. There will be a lot of output, but you can try running the following to help debug why the file cannot be opened:
cd src/kernel; strace -f mpiicc -g -std=c++11 -Wall -I/yask-master/include -I/yask-master/include/aux -I/yask-master/src/kernel/lib -I/yask-master/src/common -I/yask-master/src/contrib/coefficients -I/yask-master/build/kernel/yask_kernel.iso3dfd.avx2/gen -xCORE-AVX2 -debug extended -restrict -O3 -fopenmp -DUSE_INTRIN256 -DUSE_AVX2 -DYK_CODE_FILE=/yask-master/build/kernel/yask_kernel.iso3dfd.avx2/gen/yask_stencil_code.hpp -DALLOW_NEW_VARS=1 -DUSE_MPI -x c++ -fPIC -c -o /yask-master/build/kernel/yask_kernel.iso3dfd.avx2/obj/factory.o /yask-master/src/kernel/lib/factory.cpp
There should be a detailed error message somewhere near the end similar to this:
open("/yask-master/build/kernel/yask_kernel.iso3dfd.avx2/gen/yask_stencil_code.hpp", O_RDONLY) = -1 ENOENT (No such file or directory)
If you want, you can just put all the output into pastebin, and I can look at it.

[mengshanfeng]

@chuckyount
Many thanks!
strace.txt

[chuckyount]

This run failed with "could not checkout FLEXlm license". Not related to the earlier problem, I assume.

[mengshanfeng]

@chuckyount
Aha, i do just have a evaluation of icc (or FLEXlm ), and it seemes that it expired...

[chuckyount]

Can you try building with gcc using "make clean; make YK_CXX=gcc mpi=0 stencil=iso3dfd" just to see if it works?

[mengshanfeng]

@chuckyount
i tried, it seems it failed again...
gcc_error.txt

[chuckyount]

Sorry; try g++ specifically: "make clean; make YK_CXX=g++ mpi=0 stencil=iso3dfd"

[mengshanfeng]

@chuckyount
Many thanks!
yask_kernel.iso3dfd.avx2.make-report.txt
g++.txt

it seems that it works!

[chuckyount]

Yes, it looks like it works with g++. You can also try clang++. Perhaps there was some issue with your installation of icc or Intel MPI.