symbol not found in flat namespace '_ompi_mpi_byte'

[Jamie790]

Hi,

I have successfully build Openfoam-5.x in M2, but when i try to run simplefoam or blockmesh i get this message:

%simpleFoam dyld[1343]: symbol not found in flat namespace '_ompi_mpi_byte' zsh: abort simpleFoam

%blockMesh dyld[1654]: symbol not found in flat namespace '_ompi_mpi_byte' zsh: abort blockMesh

Can you help me to solve this problem. Many thanks.

[mrklein]

Hi,

It looks like architecture mix. By make rules were made for x86_64 (ex. wmake/rules/darwin64Clang/c++):

CC          = xcrun c++ -arch x86_64 -std=c++14

While Homebrew-installed openmpi is compiled for arm64. So, you need to either simply remove -arch x86_64 flag in wmake/rules/darwin64Clang/c++ and wmake/rules/darwin64Clang/c, or put there arm64 instead of x86_64. And then recompile the software.

[Jamie790]

Hi,

Thanks for you reply. I tired to put arm64 instead of x86_64 in wmake/rules/darwin64Clang/c++ and wmake/rules/darwin64Clang/c and then recomplied.

But i get some error message during ./Allwmake

``` /Users/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/word.HIn file included from :/Users/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/string.H42::
error: In file included from /Users/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/string.H51:51:
reference to unresolved using declarationIn file included from :
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string
In file included from :/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string527::
527:
    _VSTD::memcpy(&__r, __p, sizeof(__r));/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/hash.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/hash.h::37           ^37:
:1212::  error: error: reference to unresolved using declarationreference to unresolved using declaration

In file included from 99/Users/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/wchar.h:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/iosfwd:In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__mbstate_t.h:29:
:99/Users/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/wchar.h:
:62In file included from :/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__mbstate_t.h4262:::29 42:
: /Users/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/wchar.herror: :error: no type named 'wstring' in namespace 'std'62:42:no type named 'wstring' in namespace 'std' 

error: no type named 'wstring' in namespace 'std'
Ostream& operator<<(Ostream&, const std::wstring&);
Ostream& operator<<(Ostream&, const std::wstring&);                                    ~~~~~^

Ostream& operator<<(Ostream&, const std::wstring&);                                    ~~~~~^
                                    ~~~~~^
/Users/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/string.HIn file included from :/Users/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/int32.H51:error: :
43In file included from :
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/stringIn file included from reference to unresolved using declaration:/Users/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/word.H529:
:
42In file included from :
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__ios/fpos.hIn file included from :/Users/liqiaoqiao/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/string.H:typedef fpos<mbstate_t>    streampos;51
14             ^: 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/iosfwdIn file included from :230/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/string/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__mbstate_t.h:::4414:529:1:
 :In file included from  /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__ios/fpos.h:error: 14note: :
using declaration annotated with 'using_if_exists' here/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/iosfwdreference to unresolved using declaration:

230:14: using ::mbstate_t _LIBCPP_USING_IF_EXISTS;
typedef fpos<mbstate_t>    streampos;error: 
^
             ^reference to unresolved using declaration

In file included from UPstream.C:26/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__mbstate_t.h:
:typedef fpos<mbstate_t>    streampos;44
:1             ^:
In file included from /Users/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/UPstream.H :/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__mbstate_t.hnote: 42:
In file included from :/Users/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/labelList.H44using declaration annotated with 'using_if_exists' here
::471:

I am try to compile OpenFOAM-5.x-7f7d351b7.patch, i am not sure where i did wrong. Should i try other patches to see if there is same error? Many thanks.

[mrklein]

Well, it seems, we need more information. Could you post output of:

1. uname -m
2. file /opt/homebrew/Cellar/open-mpi/*/lib/libmpi.dylib
3. Compilation command from log-file. To see what flags are really passed to compiler.

[Jamie790]

Hi,

1. uname -m - i got arm64
2. file /opt/homebrew/Cellar/open-mpi/*/lib/libmpi.dylib - i got /opt/homebrew/Cellar/open-mpi/4.1.5/lib/libmpi.dylib: Mach-O 64-bit dynamically linked shared library arm64
3. see file attached Allwmake.docx

Many thank for your reply.

Regards, mz

[mrklein]

Things are a bit complicated, cause I do not have access to Apple's ARM platform, and I have never tried to compile 5.x with current compiler. So, I would propose:

• Try to remove -arch flag from compilation rules.
• Post output of brew doctor command. If there is a problem with clang installation, the command will shown them. Though, you have successfully compiled the code for x86_64, I doubt, there is a problem with the installation.

[nolankucd]

You should be able to fix this by installing Xcode and the Command line Tools before building OpenFOAM. Then wmake/rules/darwin64Clang/c++ and wmake/rules/darwin64Clang/c will reference -m64 and not x86-64

[philipcardiff]

FYI, I also have this issue on my M3 Mac. I am not sure of the cause of the problem, but I suspect it is related to linking to libPstream or libmpi.

I will post here if I progress, but I am happy to hear about others' experiences.

[philipcardiff]

The _ompi_mpi_byte should be given in libmpi.dylib, e.g. we can see this with nm:

>> nm -g $(mpicc --showme:link | sed -e 's/.*-L\([^ ]*\).*/\1/')/libmpi.dylib | c++filt | grep "_ompi_mpi_byte"
3233:00000000001e4808 D _ompi_mpi_byte

I am not sure why this symbol is not found, if mpi is being linked correctly, which it seems to be...

[philipcardiff]

Problem solved: your solution here works.

That is, in $WM_DIR/rules/darwin64Clang/c++ and $WM_DIR/rules/darwin64Clang/c, replace x86_64 with arm64. Then, clean (wcleanPlatform) and re-build OpenFOAM.

However, this leads to an error when compiling $FOAM_SRC/OSspecific related to #include <xmmintrin.h>. A hack fix is to comment line 41 in $FOAM_SRC/OSspecific/POSIX/signals/sigFpe.C:

//#include <xmmintrin.h>   

and comment lines 215 and 216

        // _mm_setcsr(_MM_MASK_MASK &~                                                                                    
        //            (_MM_MASK_OVERFLOW|_MM_MASK_INVALID|_MM_MASK_DIV_ZERO));  

Everything now works correctly, including in parallel.

Creating a dedicated darwinArm64Clang seems like a reasonable solution for the rules. I am not sure about the implication of the sigFpe.C hack. I see that OpenFOAM.com has solved this issue, so maybe something can be copied from there. Let me know if you like me to test or propose an updated patch.

[mrklein]

Thank you for the feedback. Yes, commented-out parts are Intel-specific.

OpenFOAM.com solved problem of sigFPE on ARM-based Macs. I will try to add the solution to OpenFOAM.org patches, though I won't be able to test them. As soon as I update the patches, I will create an issue for testing.