Clang error unsupported option fopenmp

The “clang: error: unsupported option ‘-fopenmp’” error can appear because the clang doesn’t support the -fopenmp flag and can be fixed by installing the latest versions of LLVM or clang. This article contains all the reasons for this error, solutions, and experts’ ideas. Keep reading to learn somelearnck techniques to get rid of this error.

Why Are You Getting the “Clang: Error: Unsupported Option ‘-Fopenmp’” Error?

– Clang Doesn’t Support OpenMP on Mac

If you are using Mac and facing the error “clang: error: unsupported option ‘-fopenmp,’” that is probably the provided default clang by Apple that doesn’t support Mac. You would get the error when you run the following:

Clang -fopenmp program_name.c. The error describes that your clang doesn’t support the -fopenmp flag.

– Linker Errors After Compilation

Sometimes the linker error also creates the same issues. After completing the compilation, you might see the linker error about missing the x86_64 symbol from the libomp library.

– Travis

This error can be received while deploying the project using OpenMP, you can get the ‘-fopenmp’ on Travis.

– C++

If you have multiple C++ files in your folder and run the C++ code in the terminal, you can get the “clang: error: unsupported option ‘-fopenmp’” error.

– Sparseconvnet Build Error

If you are getting this error while building SparseConvNet on Mac, this could be because your MacOS version of clang is not negatively supporting. Or changing the compiler version could also be the cause here. You can also get that error after running bash develop.sh on your terminal.

– Chempy Library

If you are working in Chempy library in Python, having the homebrew and GCC installed, and getting this issue, there could be two causes of this error.

The chempy is supported only on Linux, so it is possible that after working on your compilers, you are running neither on Mac nor on Windows. That could be one of the reasons you are getting that error.

You might not be using the correct Clang version from the Anaconda environment.

How To Fix the Error

– Clang Doesn’t Support OpenMP on Mac

If you are using Mac and getting the “clang: error: unsupported option ‘-fopenmp’” error, the cause is Apple-provided default clang doesn’t support Mac. So here, to avoid error, first of all, what you need to do is to install the latest version of LLVM, which might fix the problem.

If your problem is still not fixed, you should install the latest version of clang on your Mac that supports OpenMP by default and enable it. You need to install brew LLVM LIBOMP, but make sure that the clang version should be the latest one to compile with the -fopenmp flag.

As you download the LLVM, you have access to all the binaries in /usr/local/opt/llvm/bin. Then you should compile the OpenMP program. Put omp_ProgramNAme.c in a file and use the following extension:

/usr/local/opt/llvm/bin/clang -fopenmp -L/usr/local/opt/llvm/lib omp_ProgramName.c -o ProgramName

You might also need to set the “CPPFLAGS” with -I/usr/local/opt/llvm/include.

– Use OpenMP With Apple Clang and Homebrew Libomp

Another solution to that problem is to use the OpenMP with Apple clang and install brew libomp. You just need to replace a command like a clang -fopenmp test.c with clang -Xpreprocesssor -fopenmp test.c -lomp.

Here you might face problems in finding omp.h for inclusion. OMP is installed under /usr/local/Cellar/libomp/10.0.0/include symbolically linked to /usr/local/include. There could be any bug in the installation process, so if you are sure that you have successfully installed the libomp under Homebrew, you can ask about this issue on the Homebrew forum.

– Linker Errors After Compilation

After compilation, you should use the OpenMP with Apple clang if you have the linker error issue after compilation. For that, you need to follow a few steps as follows:

In the first step, you need to install LLVM with OpenMP and libomp with brew.

brew update

brew install llvm libomp

Then you need to add include and link directories in CMakeList.txt by using the following code:

include_directories(“/usr/local/include” “/usr/local/opt/llvm/include”)

link_directories(“/usr/local/lib” “/usr/local/opt/llvm/lib”)

Then you need to run CMake with the new compilers by the following code:

CMake -DCMAKE_C_COMPILER+”/usr/local/opt/llvm/bin/clang” -DCMAKE_CXX_COMPILER=”/usr/local/opt/llvm/bin/clang++” ..

This is how you can install the latest version of Clang.

You can also use brew –prefix llvm if you don’t want to assume /usr/local/opt/llvm.

– Travis

If you are working on Travis and getting the “clang: error: unsupported option ‘-fopenmp’” error, you should know that Apple’s LLVM doesn’t support -fopenmp. You should use brew’s LLVM. This is how you can link OpenMP

brew install llvm libomp

export CPP=/usr/local/opt/llvm/bin/clang;

– C++

If you are working on C++ code and getting the same error; first of all, what you need to do is to install the libomp with homebrew by using:

brew install libomp

And then you can compile an OpenMP with this:

clang -Xpreprocessor -fopenmp -I/usr/local/include -L/usr/local/lib -lomp main.c -o main

You would also want the following:

Clang++ -Xpreprocessor -fopenmp -I/usr/local/include -L/usr/local/lib -lomp main.cpp -o main

– SparseConvNet Build Error

If you are getting this error while building SparseConvNet on Mac, you should follow the same solution given above in this article in the “clang doesn’t support OpenMP on Mac” portion.

– Chempy Library

First of all, you need to install homebrew by using this:

/usr/local/bin/g++-10

Now you have to make sure what is installed and where it is installed using this:

brew ls gcc

Then, you can use the following to find the symlinked binaries that you should be using

Cs /usr/local/bin

ls -1 | grep gcc

First, you need to determine what compiler you want to use and then tell your build tool how to use it. Make sure you are using the correct package to use Hebrew.

To find out the different compilers, you can use the following methods:

• CMake: CXX=/usr/local/bin/g++-10 cmake ..
• Make: make CXX=/usr/local/bin/g++-10
• Autconf: ./configure CXX=/usr/local/bin/g++-10

FAQs

– What Is Openmp Support?

OpenMP is not any software or a tool, it’s an API, or you can say that it is a set of directives for programs written in C, C++, or FORTRAN. The OpenMP stands for open source multi-processing. OpenMP is used for multi-threading. OpenMP finds out those blocks of codes that can run in parallel. OpenMP is also called a shared memory model and Fork-join model.

– How Does OpenMP Work?

It starts with one main thread in each process, so first of all, we create one main thread. That one main thread is called the master thread. Then at some part of the program, we require multip-threading, so we make multiple threads. All threads other than master threads are called slave threads.

Once slave threads have completed their work, they give their result back to their master thread. So again, our process is completed in a single thread. As these multiple threads share the memory of the primary process, and that is the reason the OpenMP is also called the shared memory model. The below example explains how you can use the OpenMP for C or C++ language.

– Example of Using OpenMP for C or C++ Language

First, we have to include a header file “omp.h”, so all the functions related to OpenMP have a defined “omp.h” header. Make sure to mention the preprocessor directive, and then you can create a simple statement in C or C++ language. Here is the preprocessor directive in “#pragma omp parallel.”

Now suppose we want to create multiple threads, but the question is, how many threads can be made? Well, the default number of threads created is equal to the number of processor cores. That means if you have i3, i5, or i7 processor, by default, it has four cores, and if a processor has four cores, the preprocessor directive statement will create four threads.

If we want to create, we need to add “num_threads(5)”. Here we assigned ‘5’ so five threads would be made. So here we have five threads, and all of them are in the form of that simple statement. All five threads will run simultaneously and do the same task.

– What Is Clang in Mac?

Clang is a compiler that is used in front-end development. It compiles the C, C++, Objective C++, and Objective C programming languages into machine codes. Clang is also used for frameworks like OpenMP, OpenCL, CUDA, HIP, and RenderScript.

For the back end, the Clang uses the LLVM compiler.

– How Does Clang Work?

The clang is designed to work like other compilers. There are three stages for the Clang to work.

The first stage is all about the front-end, where the compiler is used to parse source code. The compiler identifies errors and builds the AST to work as an input code. The second stage optimizes the generated AST. At the same time, the third stage is all about the back end. Here, the compiler generates the final code that the machine will execute.

Conclusion

Let’s conclude what we learned today:

• There could be many causes of this problem but the important one is you clang would not be supporting OpenMP on Mac.
• The latest LLVM and Clang version that supports OpenMP is essential to avoid this error.
• Installing libomp with brew is a must case to solve this error.

We covered why the “clang: error: unsupported option ‘-fopenmp’” you are getting, and all the possible causes of that problem along with solutions. Now you can get rid of that error as you have this article, and you can find out the cause of your case and the respective solution.

Comments

* add init_score & test cpp and python result consistency

* try fix common.h

* Fix tests (#3)

* update atof

* fix bug

* fix tests.

* fix bug

* fix dtypes

* fix categorical feature override

* fix protobuf on vs build (#1004)

* [optional] support protobuf

* fix windows/LightGBM.vcxproj

* add doc

* fix doc

* fix vs support (#2)

* fix vs support

* fix cmake

* fix #1012

* [python] add network config api  (#1019)

* add network

* update doc

* add float tolerance in bin finder.

* fix a bug

* update tests

* add double torelance on tree model

* fix tests

* simplify the double comparison

* fix lightsvm zero base

* move double tolerance to the bin finder.

* fix pylint

* clean test.sh

* add sklearn test

* remove underline

* clean codes

* set random_state=None

* add last line

* fix doc

* rename file

* try fix test

I had the same problem.

sudo apt install libomp-dev

Fixed it with Ubuntu 16.10

//test.c
#include "omp.h"
#include <stdio.h>

int main(void) {
  #pragma omp parallel
  printf("thread %dn", omp_get_thread_num());
}

Then

clang test.c -fopenmp
./a.out
thread 0
thread 5
thread 2
thread 1
thread 7
thread 3
thread 4
thread 6

Also

clant-3.9 test.c -fopenmp

works.

GCC and Clang use different OpenMP runtime libraries : libgomp and libomp respectivly.

Clang’s runtime is the LLVM OpenMP runtime which in turn is based on the Intel OpenMP runtime (which is open source).
https://www.openmprtl.org/

On my system GCC installed omp.h at

/usr/lib/gcc/x86_64-linux-gnu/6/include/omp.h

and libomp-dev insalled omp.h at

/usr/include/omp.h

These are different header files which include different function definitions. It may be okay to use either header file for e.g. omp_get_wtime() but in general I think it’s probably better to use the header file that corresponds to the runtime that is linked to.

clang: error: unsupported option ‘-fopenmp’ #16

Hi, thanks for this great work.

I noticed it doesn’t compile on OSX (using clang), «make» gives these errors:

[dep] third-party/lodepng/lodepng.cc .
clang: error: unsupported option ‘-fopenmp’
[dep] stitch/warp.cc .
clang: error: unsupported option ‘-fopenmp’
[dep] stitch/transform_estimate.cc .
clang: error: unsupported option ‘-fopenmp’
[dep] stitch/stitcherbase.cc .
clang: error: unsupported option ‘-fopenmp’

Compiling with gcc on Ubuntu (and probably OSX if installed gcc) works ok.

Any ideas what to fix in the makefile for clang?

The text was updated successfully, but these errors were encountered:

Clang starts supporting openmp at some version. Works for me with clang on
Linux.

On Aug 3, 2016 11:00 AM, «Jouni Helminen» notifications@github.com wrote:

Hi, thanks for this great work.

I noticed it doesn’t compile on OSX (using clang), «make» gives these
errors:

[dep] third-party/lodepng/lodepng.cc .
clang: error: unsupported option ‘-fopenmp’
[dep] stitch/warp.cc .
clang: error: unsupported option ‘-fopenmp’
[dep] stitch/transform_estimate.cc .
clang: error: unsupported option ‘-fopenmp’
[dep] stitch/stitcherbase.cc .
clang: error: unsupported option ‘-fopenmp’

Compiling with gcc on Ubuntu (and probably OSX if installed gcc) works ok.

Any ideas what to fix in the makefile for clang?

—
You are receiving this because you are subscribed to this thread.
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From my dealings with it, the clang on OSX is an Apple-customized one one that doesn’t have OpenMP support. Changing the makefile or even the build system entirely (e.g. to cmake) doesn’t help at all. As you have suggested yourself, the only way you can get around this issue is to get another compiler (latest clang or gcc) as well as their associated libraries and then try building the project again.

Thanks @GitZChen ! I should add these to the readme.

You are right, latest clang should have OpenMP support, but doesn’t (yet) on MacOS. I installed Xcode 8 Beta 4 and it didn’t include any updates to clang/LLVM version (but perhaps MacOS Sierra will).

So after a bit of fiddling, here is how to successfully compile OpenPano on MacOS El Capitan:

1. Install brew (http://brew.sh/)
2. «brew install gcc —without-multilib» (grab a coffee, this takes quite a while — but needed because default brew installation of gcc doesn’t have OpenMP support)
3. «export CXX=/usr/local/Cellar/gcc/6.1.0/bin/g++-6» (use the path from the output of brew gcc install. at the time of writing the above is correct, but may change. Do this or otherwise osx still uses clang to compile)
4. «brew install eigen»
5. run «make» in panorama /src — it compiles OK now

For 3, you can maybe try using «brew ls gcc» to list all installed components in the gcc formula then determine the path of g++ binary.

Also, in case anyone really wants to use clang instead of gcc, just substitute «gcc» with «llvm» and the path to «g++-6» with the path to the brew-installed «clang++» in the above instructions.

Though @jounih, don’t you still need libjpeg?

I am following this thread, and tried the method suggested by @jounih, compiling . However I got many of these errors:

/var/folders/5_/k6wvp3594651b83cz4f_f4n80000gn/T//cc2ALrIr.s:1205:no such instruction: vmovaps %xmm0, -160(%rbp)’ /var/folders/5_/k6wvp3594651b83cz4f_f4n80000gn/T//cc2ALrIr.s:1206:no such instruction: vmovaps %xmm1, -144(%rbp)’
/var/folders/5_/k6wvp3594651b83cz4f_f4n80000gn/T//cc2ALrIr.s:1207:no such instruction: vmovaps %xmm2, -128(%rbp)’ /var/folders/5_/k6wvp3594651b83cz4f_f4n80000gn/T//cc2ALrIr.s:1208:no such instruction: vmovaps %xmm3, -112(%rbp)’

Did a quick look on Google, and looks like it is related to AVX on OSX problem. I’ve tried several methods suggested but no luck. Have you ever encountered this issue?

My machine is an 2013 MBP with i5. I did a check and it does have AVX1.0.

Never encountered that problem before compiling GCC. Though isn’t this question off-topic for OpenPano? Maybe you’ll have better luck asking it on SO instead?

How can I perform step 5 of jounih ‘s comment?

I know this is a bit old, but just in case someone is still looking for the solution, I want to say that the solution given by @jounih fixed the same problem I had. Just make sure that you get the right path of ‘/usr/local/Cellar/gcc/6.1.0/bin/g++-6’ for the export. By the time of commenting, mine was «export CXX=»/usr/local/Cellar/gcc/7.2.0/bin/g++-7»

In jounih’s commented on Aug 4, 2016 •
In step 5 «run «make» in panorama /src — it compiles OK now»

what is panorama ? where is /src ?
When I run «make» , I get «make: *** No targets specified and no makefile found. Stop.»

what is above link referring to ?

Hello ppwwyyxx , I need to run step 5 as i stated above.
Sorry I am unable to following from link you gave. Could you please describe what should I do now ?

You are right, latest clang should have OpenMP support, but doesn’t (yet) on MacOS. I installed Xcode 8 Beta 4 and it didn’t include any updates to clang/LLVM version (but perhaps MacOS Sierra will).

So after a bit of fiddling, here is how to successfully compile OpenPano on MacOS El Capitan:

1. Install brew (http://brew.sh/)
2. «brew install gcc —without-multilib» (grab a coffee, this takes quite a while — but needed because default brew installation of gcc doesn’t have OpenMP support)
3. «export CXX=/usr/local/Cellar/gcc/6.1.0/bin/g++-6» (use the path from the output of brew gcc install. at the time of writing the above is correct, but may change. Do this or otherwise osx still uses clang to compile)
4. «brew install eigen»
5. run «make» in panorama /src — it compiles OK now

Could you please help me run step 5 ? I did till 4. No clue about step 5 ?
I get below
«make: *** No targets specified and no makefile found. Stop.»
No clue where is «panorama /src» ?

@ppwwyyxx dude, I did all 5 steps but it still is returning the error «unsupported option -fopenmp» 🙁
I’ve reiinstalled the gcc and set the env variable but it is still returning the error

After runing «make -C src» this is the error:

Answering @tpsmahal step 5 can be executed with: «make -C src»

Источник

clang: error: unsupported option ‘-fopenmp’ #64

Upgraded to R 3.4.0, «You Stupid Darkness». When building on Mac I now receive:

clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o vcfR.so NM2winNM.o RcppExports.o ad_frequency.o extractGT2NM.o freq_peak.o gt_to_popsum.o is_het.o masplit.o pair_sort.o rank_variants.o seq_to_rects.o var_window.o vcfRCommon.o vcf_io.o -fopenmp -lgomp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: error: unsupported option ‘-fopenmp’
make: *** [vcfR.so] Error 1
ERROR: compilation failed for package ‘vcfR’

The text was updated successfully, but these errors were encountered:

Note that it appears to be building at CRAN with 3.40, so this is likely specific to my system.

Hi Brian, I ran into a similar issue. If it helps, I’m posting the way I was able to fix it on my machine. If it doesn’t help, then feel free to ignore/delete this.

CRAN has updated to clang 4.0, which is not distributed for OSX. I downloaded clang from r.research.att.com/libs.

The instructions are to un-tar it to / , where it would install at /usr/local/clang4 . Because of the permissions issues in Sierra, I always got an error that it couldn’t modify /usr/ even though Apple says it’s okay to install things into /usr/local , so I un-tar’d it where it was, and moved the output from ./usr/local/clang4 to /usr/local/clang4 .

As suggested by CRAN, I then modified my

/.R/Makevars file to the following (as specified by CRAN):

The clang version sounds spot on! But now I’m generating a segmentation fault. I suspect it has something to do with the contents of my

/Makevars. Perhaps some quality time on writing R extensions will help me sort that out.

I reinstalled all of my packages and now I only have segmentation faults when I use devtools, but I can’t seem to figure out what’s triggering it. It is quite frustrating 😣

Do your segfaults look something like this by any chance

But I’m afraid its a bit mysterious to me. I want to believe it is compiling.

Well, I went scorched earth and removed most of my packages and re-installed them. From R:

And reinstall. Now vcfR magically builds and passes all tests. Zero points for elegance, but it worked. And for the record, my

.R/Makevars file now looks like:

And as a reminder, this is Mac (OSX) specific.

Источник

error: unsupported option ‘-fopenmp’ #789

«error: unsupported option ‘-fopenmp’»

When I try to install the package on the MacOS according to the guidance, it showed the following error.

c++ -g -O3 -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -I./include -I./htslib -I./minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -MM src/nanopolish_call_methylation.cpp src/nanopolish_call_variants.cpp src/nanopolish_extract.cpp src/nanopolish_getmodel.cpp src/nanopolish_haplotype.cpp src/nanopolish_index.cpp src/nanopolish_methyltrain.cpp src/nanopolish_phase_reads.cpp src/nanopolish_polya_estimator.cpp src/nanopolish_raw_loader.cpp src/nanopolish_read_db.cpp src/nanopolish_scorereads.cpp src/nanopolish_squiggle_read.cpp src/nanopolish_train_poremodel_from_basecalls.cpp src/nanopolish_variant_db.cpp src/nanopolish_vcf2fasta.cpp src/training_core.cpp src/hmm/nanopolish_duration_model.cpp src/hmm/nanopolish_profile_hmm.cpp src/hmm/nanopolish_profile_hmm_r7.cpp src/hmm/nanopolish_profile_hmm_r9.cpp src/hmm/nanopolish_transition_parameters.cpp src/common/fs_support.cpp src/common/logsum.cpp src/common/nanopolish_alphabet.cpp src/common/nanopolish_bam_processor.cpp src/common/nanopolish_bam_utils.cpp src/common/nanopolish_common.cpp src/common/nanopolish_iupac.cpp src/common/nanopolish_klcs.cpp src/common/nanopolish_variant.cpp src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/pore_model/nanopolish_model_names.cpp src/pore_model/nanopolish_pore_model_set.cpp src/pore_model/nanopolish_poremodel.cpp src/io/nanopolish_fast5_io.cpp src/io/nanopolish_fast5_loader.cpp src/io/nanopolish_fast5_processor.cpp src/thirdparty/fet.c src/thirdparty/stdaln.c src/thirdparty/scrappie/event_detection.c src/thirdparty/scrappie/scrappie_common.c > ./.depend;
clang: warning: treating ‘c’ input as ‘c++’ when in C++ mode, this behavior is deprecated [-Wdeprecated]
clang: warning: treating ‘c’ input as ‘c++’ when in C++ mode, this behavior is deprecated [-Wdeprecated]
clang: warning: treating ‘c’ input as ‘c++’ when in C++ mode, this behavior is deprecated [-Wdeprecated]
clang: warning: treating ‘c’ input as ‘c++’ when in C++ mode, this behavior is deprecated [-Wdeprecated]
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
clang: error: unsupported option ‘-fopenmp’
make: *** [.depend] Error 1

I wonder what should I do with that? I am sorry since I am new to bioinformatics without any prior knowledge in computing.

Thank you very much for helping1

The text was updated successfully, but these errors were encountered:

See #279. This is usually a problem on the Mac, because the compiler that comes with it doesn’t have OpenMP enabled. You can use https://brew.sh (Homebrew) to install gcc.

brew install gcc

Then you can find all the versions of GCC you’ve installed

At the time of this comment this should be gcc-9 . So you need to compile with

make CXX=g++-9 CC=gcc-9

I see. Thank you very much for helping! The problem is solved!

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Источник

clang: error: unsupported option ‘-fopenmp’ on Mac OS #3

I tried to run order «python setup.py build» on Mac OS 10.12.3, and got the error
clang: error: unsupported option ‘-fopenmp’

I tried export CC=/usr/bin/gcc, gcc-6, clang or llvm-gcc, they all don’t work.

for gcc-6 case, I got different error:
gcc-6: error: unrecognized command line option ‘-Wshorten-64-to-32’

Has anyone encountered the same issue?

The text was updated successfully, but these errors were encountered:

Yes I am facing the same issue. Any resolution found?

So far no good news. I chose to run pypoisson on a linux system, which separated my code into two parts.

Hope you good luck 🙂

I wanted it for R tool support. So I switched to lower version of R and resolved the issues.

I just ran into this problem, I will try to find a solution by my own. But if anyone got a solution in the meantime, I am interested 🙂

I just tried to install the package as well from a mac. I managed to install but am still not able to run the examples.

I have previously installed gcc and g++ with homebrew. Then, exporting and aliasing them, as
export CC=/usr/local/bin/gcc-8
export CXX=/usr/local/bin/g++-8
alias gcc=‘/usr/local/bin/gcc-8’
alias g++=‘/usr/local/bin/g++-8’

enables me to succesfully run

python setup.py build
python setup.py install

after modifying the first line of pypoisson.pyx,
#cython: language_level=3str
to
#cython: language_level=3

However, running python test.py halts to the error
Traceback (most recent call last):
File «test.py», line 1, in
from pypoisson import poisson_reconstruction
ImportError: dlopen(/anaconda3/lib/python3.6/site-packages/pypoisson.cpython-36m-darwin.so, 2): Symbol not found: _GOMP_parallel
Referenced from: /anaconda3/lib/python3.6/site-packages/pypoisson.cpython-36m-darwin.so
Expected in: flat namespace
in /anaconda3/lib/python3.6/site-packages/pypoisson.cpython-36m-darwin.so

and so far I haven’t been able to advance from here.
When it says this has been tried on OSX, I wonder how and what is the environment like?

Источник

Hi all,

I am having an installation error with opencarp where when I try to build using cmake I get the following error: 

p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo; color: #000000}
p.p2 {margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo; color: #5620f4}
p.p3 {margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo; color: #000000; min-height: 13.0px}
span.s1 {font-variant-ligatures: no-common-ligatures}
span.s2 {font-variant-ligatures: no-common-ligatures; color: #000000}
span.s3 {font-variant-ligatures: no-common-ligatures; color: #ca3323}

macbook-pro-82:openCARP sushruthmanchineella$ cmake —build _build

[ 10%] Built target param

[ 12%] Built target param-bin

[ 13%] Built target carp

[ 17%] Built target numerics

[ 19%] Built target fem

[ 68%] Built target limpet

[ 70%] Built target physics

[ 71%] Built target simulator

[ 71%] Built target opencarp-bin

[ 75%] Built target bench-bin

[ 76%] Built target igbutils_common

[ 78%] Built target igbapd-bin

[ 80%] Built target igbextract-bin

[ 82%] Built target muparser

[ 85%] Built target igbops-bin

[ 86%] Built target igbhead-bin

[ 87%] Built target mesher

[ 89%] Built target mesher-bin

[ 90%] Performing update step for ‘meshtool’

[ 90%] No patch step for ‘meshtool’

[ 90%] No configure step for ‘meshtool’

[ 91%] Performing build step for ‘meshtool’

* compiling: modes/clean_mode.cpp

* compiling: modes/convert_mode.cpp

* compiling: modes/collect_mode.cpp

* compiling: modes/extract_mode.cpp

* compiling: modes/generate_mode.cpp

* compiling: modes/interpolate_mode.cpp

* compiling: modes/insert_mode.cpp

* compiling: modes/itk_mode.cpp

clangclangclangclangclang: clangclang: : : : clang: : : errorerror: errorerror: : error: : error: error: error: unsupported option ‘-fopenmp’

unsupported option ‘-fopenmp’unsupported option ‘-fopenmp’unsupported option ‘-fopenmp’

unsupported option ‘-fopenmp’

unsupported option ‘-fopenmp’

unsupported option ‘-fopenmp’

unsupported option ‘-fopenmp’

make[4]: *** [modes/clean_mode.o] Error 1

make[4]: *** Waiting for unfinished jobs….

make[4]: *** [modes/collect_mode.o] Error 1

make[4]: *** [modes/extract_mode.o] Error 1

make[4]: *** [modes/generate_mode.o] Error 1

make[4]: *** [modes/insert_mode.o] Error 1

make[4]: *** [modes/interpolate_mode.o] Error 1

make[4]: *** [modes/itk_mode.o] Error 1

make[4]: *** [modes/convert_mode.o] Error 1

make[3]: *** [parbuild] Error 2

gmake[2]: *** [external/CMakeFiles/meshtool.dir/build.make:86: external/meshtool/src/meshtool-stamp/meshtool-build] Error 2

gmake[1]: *** [CMakeFiles/Makefile2:825: external/CMakeFiles/meshtool.dir/all] Error 2

gmake: *** [Makefile:156: all] Error 2

I am running python 3.8 and have also run brew install llvm as well as installed and linked g++. Please let me know if anyone knows how to correct this error.