I'm building a project from github (https://github.com/marsicoLab/PROmiRNA) and have the following requirements on my mac (Big Sur 11.4); gcc 9.4, cmake 3.21.1, R 4.1.0.
After using cmake, which runs without error, I use make however this gives me the below errors:
clang: error: unable to execute command: Segmentation fault: 11
clang: error: clang frontend command failed due to signal (use -v to see invocation)
Apple clang version 12.0.5 (clang-1205.0.22.9)
Target: x86_64-apple-darwin20.5.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
clang: note: diagnostic msg: Error generating preprocessed source(s).
make[2]: *** [CMakeFiles/PROmiRNA.dir/PROmiRNA.cpp.o] Error 254
make[1]: *** [CMakeFiles/PROmiRNA.dir/all] Error 2
make: *** [all] Error 2
A lot of other questions online with the same issue refer to XCode but I don't have it installed and am not a developer myself so don't think I need it..?
If anyone has any suggestions I'd really appreciate it, thanks :)
Related
I cloned the latest version of the Poco libraries source code on to my Mac and attempted to build it per the instructions using CMake. Everything proceeded fine until it reached a point where it was trying to link the libPocoCrypt.dylib library. Even though the C++ compilation worked with out error, the link resulted in the following output
ld: cannot link directly with dylib/framework, your binary is not an allowed client of /usr/lib/libcrypto.dylib for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [lib/libPocoCrypto.80.dylib] Error 1
make[1]: *** [Crypto/CMakeFiles/Crypto.dir/all] Error 2
make: *** [all] Error 2
Doing some research, I discovered that Apple doesn't want applications linking against its libcrypto library and thus, the resulting error messages. The question then is, what do I need to do here to make this work?
I am trying to install Elemental. I cloned it from the GitHub directory. Made a build directory and ran cmake command in it. But when I do a make, it shows the following error message:
[ 73%] Linking CUDA device code
CMakeFiles/EntrywiseMap.dir/cmake_device_link.o
nvcc fatal : Unknown option 'pthread'
tests/CMakeFiles/EntrywiseMap.dir/build.make:99: recipe for target
'tests/CMakeFiles/EntrywiseMap.dir/cmake_device_link.o' failed
make[2]: *** [tests/CMakeFiles/EntrywiseMap.dir/cmake_device_link.o]
Error 1
CMakeFiles/Makefile2:1506: recipe for target
'tests/CMakeFiles/EntrywiseMap.dir/all' failed
make[1]: *** [tests/CMakeFiles/EntrywiseMap.dir/all] Error 2
Makefile:140: recipe for target 'all' failed
make: *** [all] Error 2
I am using ubuntu 18, with cuda 10 and cmake version 3.13.4
What's the version of Cmake? This issue seems to be on CMake 3.12 and fixed on CMake 3.13
For me moving to the newer version of CMake 3.14.0 helped get past the issue.
I compiled my makefile for my C++ program on my Mac and it compiled just fine. I tried doing the same thing on my Linux machine with the exact same files and got:
/usr/bin/ld: cannot find -lc++abi
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [allocate-asan] Error 1
I do not know how I can go about compiling this on my linux machine with this error. Any ideas?
I'm aiming to install openmpi 1.6.5 on my Macbook Pro, mountainlion 10.8.5, by following the straightforward guidelines at:
https://wiki.helsinki.fi/display/HUGG/Installing+Open+MPI+on+Mac+OS+X
While configuring with
./configure --prefix=/usr/local/bin F77=gfortran FC=gfortran
is successful, "make all" fails with:
clang: warning: argument unused during compilation: '-fopenmp'
CXXLD vtfilter
ld: library not found for -lgomp
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[7]: *** [vtfilter] Error 1
As a complete newbie, I'm stuck on this error... I read about it error here:
Error enabling openmp - "ld: library not found for -lgomp" and Clang errors
(sorry for the new thread on possibly the same issue--this website's instructions guided me to not post a new question as an answer to an old thread...)
I'm not sure if these fixes apply here (?)-- I've tried the ordering within $PATH, which had no effect. Does this look like I have an issue with my compilers? If there is more useful information I can post, please let me know.
Thank you for your time and help!
It would be much easier if you simply disable building of the bundled VampirTrace library:
$ ./configure --enable-contrib-no-build=vt ...
If you still need to trace and profile your MPI applications, you could download VampirTrace and build it separately.
jcykdeMacBook-Pro:mdrpdt-2.0.1.21 jcyk$ make
Building bin/lib/serial/APPLE-64bit/g++/libutility.a
clang: error: unknown argument: '-fforce-addr' [-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
make[1]: *** [../../build/utility/serial/APPLE-g++/64bit/release/application.o] Error 1
make: *** [bin/lib/serial/APPLE-64bit/g++/libutility.a] Error 2
I got mdrpdt from http://ritchielab.psu.edu/software/mdr-download.
how can I do to fix this?
It looks like you just need to remove -fforce-addr from the invocation of clang, see example here where configure is patched.