I am trying to build GROMACS with icc compiler but it is throwing error I have provided the error below.
": internal error: 0_76
compilation aborted for /global/scratch/groups/hpcperf/2022_Refresh/gromacs/api/nblib/topology.cpp (code 4)
make[2]: *** [api/nblib/CMakeFiles/nblib.dir/build.make:216: api/nblib/CMakeFiles/nblib.dir/topology.cpp.o] Error 4
Any help appreciated!
A sample reproducer would help us resolve your issue from our end. However, GROMACS no longer supports Intel classic compilers (icc/icpc). It supports only the Intel LLVM compilers (icx/icpx).
I had the same issue and can confirm that it is resolved when switching from the classic compilers to the LLVM compilers. Note that if you use MPI, you also need to change the compiler for these wrappers, either via the I_MPI_CC(X) environment variable or the -cc / -cxx option.
Related
I'm kinda new to the world of Intel's HPC toolchain and I'm facing some troubles making even simple DPC++ application to work when gtest is used as a testing framework
This is the CMakeLists "structure" I'm following
cmake_minimum_required(VERSION 3.14)
project(foo)
set(CMAKE_CXX_COMPILER "dpcpp")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17 -O3 -fsycl")
# add executables
# target linked libraries
# ...
option(ENABLE_TESTS ON)
if(ENABLE_TESTS)
FetchContent_Declare(
googletest
GIT_REPOSITORY https://github.com/google/googletest.git
GIT_TAG release-1.11.0
)
set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
FetchContent_MakeAvailable(googletest)
add_subdirectory(tests)
endif()
If I remove the last block, it compiles and runs as expected, otherwise I get the following error:
CMake Error at build/_deps/googletest-src/CMakeLists.txt:10 (project):
The CMAKE_CXX_COMPILER:
dpcpp
is not a full path and was not found in the PATH.
Tell CMake where to find the compiler by setting either the environment
variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path
to the compiler, or to the compiler name if it is in the PATH.
-- Configuring incomplete, errors occurred!
See also "/home/u141905/foo/build/CMakeFiles/CMakeOutput.log".
See also "/home/u141905/foo/build/CMakeFiles/CMakeError.log".
You have changed variables that require your cache to be deleted.
Configure will be re-run and you may have to reset some variables.
The following variables have changed:
CMAKE_CXX_COMPILER= /usr/bin/c++
-- Generating done
CMake Generate step failed. Build files cannot be regenerated correctly.
make: *** [Makefile:2: all] Error 1
Please notice that dpcpp is correctly set, in fact I'm using Intel's devcloud platform.
Setting CXXto the output of whereis dpcpp produces the same error.
The only "workaround" (I doubt it is one though) I found is using clang++ instead (the version from Intel's llvm). Any help or suggestion is much appreciated, thanks in advance!
EDIT: after some more attempts, I noticed that if I set CMAKE_CXX_COMPILER just after fetching gtest, everything works fine. Anyway I don't understand why this happens and how can be properly fixed.
Use the path for dpcpp binary for setting the CMAKE_CXX_COMPILER instead of using"set(CMAKE_CXX_COMPILER "dpcpp")". After adding the path("/opt/intel/oneapi/compiler/2022.0.1/linux/bin/dpcpp") to the CMAKE_CXX_COMPILER, you can run the program successfully.
Please find the below CMakeLists.txt for setting the CMAKE_CXX_COMPILER:
project(foo)
set(CMAKE_CXX_COMPILER "/opt/intel/oneapi/compiler/2022.0.1/linux/bin/dpcpp")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17 -O3 -fsycl")
# add executables
# target linked libraries
# ...
set(ENABLE_TESTS ON)
include(FetchContent)
if(ENABLE_TESTS)
FetchContent_Declare(
googletest
GIT_REPOSITORY https://github.com/google/googletest.git
GIT_TAG release-1.11.0
)
set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
FetchContent_MakeAvailable(googletest)
add_subdirectory(tests)
endif()
Thanks & Regards,
Hemanth
Did you run the source /opt/intel/oneapi/setvars.sh intel64 script? I.e. is dpcpp on your path before running cmake?
I am trying to add the BlossomV package in Julia. I am receiving the following error:
*LoadError: BlossomV not properly installed. Please run Pkg.Build("BlossomV")
LoadError: Failed to precompile BlossomV*
On running Pkg.Build("BlossomV"),
I am getting the following error:
*LoadError: IOError: could not spawn setenv(*A lot of attributes are there here*): no such file or directory (ENOENT)*
I am facing this error on both Windows 10 and Ubuntu.
I would appreciate it if anyone could explain what the issue is and how to solve it. Thank you.
BlossomV.jl is just a wrapper around a C library and I bet it is the process of building the C library that's failing. BlossomV is designed around the old approach to handling binary dependencies. It would be great to either rewrite it using pure Julia, or use the modern "artifact" system which is a vastly more robust way to ship binary dependencies.
Reaching out to the wider group as I am totally stumped trying to install Intel MPSS 4.x for my Xeon Phi 7220P.
I followed the precise steps in this link: Intel MPSS Linux User Guide Rev 4.4.1, and did it 3 times to make sure I wasn't missing any steps or making mistakes, but keep getting the following error readout:
modprobe: WARNING: Module mic_x200_dma not found.
modprobe: WARNING: Module scif_bus not found.
modprobe: WARNING: Module vop_bus not found.
modprobe: WARNING: Module cosm_bus not found.
modprobe: WARNING: Module scif not found.
modprobe: WARNING: Module vop not found.
modprobe: WARNING: Module mic_cosm not found.
modprobe: WARNING: Module mic_x200 not found.
As a result of this, I cant do the basic MPSS commands such as micctrl -s etc nor use the Xeon Phi whatsoever.
I am running Centos 7 (862 kernel), and know its not listed in the Intel pdf, but did not think this should be causing an issue as it seems that the above kernel modules are simply not being installed seemingly from Intel MPSS - but not sure if this diagnosis is correct.
Would appreciate your help - many thanks in advance!
It is complaining about that because at one point your kernel got updated from 3.10.0-514.el7 to a later version, (it happens automatically when you do a yum update, annoying I know)
Check your kernel version by running
uname -r
When you installed/compiled all the modules they were placed into /lib/modules/3.10.0-514.el7.x86_64 which is where the source code you have exported to.
You have 2 options:
Recompile the source code to work for your current kernel version (which is a pain and has it's own problems)
Revert your host kernel back to 3.10.0-514.el7 via grub config (example here) and everything will work nicely
I too struggled with this very much in the beginning and I had to read pretty much every line of source code and spend countless hours debugging until I found out. At this point there is nothing I do not know about the Xeon Phi x100/x200.
The documentation is not bad, but it didn't cover this bare essential, which is frustrating.
I have tried running the Openmdao paraboloid tutorial as well as benchmarks and I consistently receive the same error which reads as following:
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash
---------------------------------------------------------------------
MPI_abort was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 59.
NOTE: invoking MPI_ABORT causes MPI to kill all MPI processes.
you may or may not see output from other processes, depending on exactly when Open MPI kills them.
I don't understand why this error is occurring and what I can do to be able to run OpenMDAO without getting this error. Can you please help me with this?
Something has not gone well with your PETSc install. Its hard to debug that from afar though. It could be in your MPI install, or your PETSc install, or your petsc4py install. I suggest not install PETSc or PETSc4Py through pip though. I've had mixed success with that. Both can be installed from source without tremendous difficulty.
However, to run the tutorials you don't need to have PETSc installed. You could remove those packages and the tutorials will run correctly in serial for you
I'm trying to build a simple application that uses ffmpeg's libav* libraries in xcode 4 and getting the following error:
ld: illegal text reloc to non_lazy_ptr from /ffmpeg/temp/ffmpeg-0.8/builduni/lib/libavcodec.a(ac3.o) in _ff_ac3_bit_alloc_calc_psd for architecture i386
I've already tried to run ranlib -c libavcodec.a to fix this problem, but nothing happend.
One more thing: my libav* libraries are fat binaries (i386 + x86_64).
Any ideas what can it be?
I have the same error. Finally, I got the solution at
http://lists.apple.com/archives/unix-porting/2008/Jan/msg00027.html
just add other link flag:
-read_only_relocs suppress
* EXPLANATION * The two assembly commands load the absolutes address of _trail into R15. Doing so is fine if _trail is ultimately
in the same linkage unit. _trail is in libmodule.dylib. For this to
work, at runtime the dynamic loader (dyld) would have to rewrite the
two instructions. Normally dyld only updates data pointers. One work
around is to make libdyalog an archive (e.g. libdyalog.a) and link
that with pere.s. Then all the code would be in the same linkage unit,
so there would be no need for runtime text relocs. The runtime (dyld)
does support text relocs (updating instructions) for i386, but you
need to link with -read_only_relocs suppress.