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Anthony_A_1
Beginner
159 Views

Apple OS X 10.9: ld: warning: can't find atom for N_GSYM stabs

Greetings:

The following warning doesn't appear to cause any problems however I'd like to understand how to fix it. When I link an application on Apple OS X 10.9.5 with up-to-date Intel C++ I receive the following warnings.

ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal9FreeBlock12minBlockSizeE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal13BackRefMaster6dataSzE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal10MemoryPool18defaultGranularityE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal5Block16emptyEnoughRatioE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal18minLargeObjectSizeE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector23mallocRecursionDetectedE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal10MemoryPool15memPoolListLockE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal9hugePagesE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector9rmc_mutexE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector12owner_threadE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector10autoObjPtrE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)

A typical build line resembles the following excerpt (I inserted line breaks for readability).

/usr/bin/icpc   -DHAVE_LAPACK_CONFIG_H -DLAPACK_COMPLEX_STRUCTURE 
-fPIC -axCORE-AVX2,AVX,SSE4.2 -restrict -static-intel -fp-model fast=2 -ip 
-O3 -DNDEBUG -I/path/to/hdf5-1.8.6_intel-15.0_osx-10.9/include 
-I/path/to/yaml-cpp-0.5.1_intel-15.0_osx-10.9/include 
-I/path/to/boost-1.57.0_intel-15.0_osx-10.9/include 
-I/path/to/lapack-3.5.0_intel-15.0_osx-10.9/include 
-I/opt/intel/composer_xe_2015.1.108/mkl/include/fftw 
-I/path/to/Build -I/path/to/Source -I/path/to/Source/Base     
-openmp -o /path/to/AppMain.cxx.o -c /path/to/AppMain.cxx

The link line is shown below (with some entries on their own lines for convenience).

/usr/bin/icpc   -fPIC -axCORE-AVX2,AVX,SSE4.2 -restrict -static-intel -fp-model fast=2 -ip -O3 -DNDEBUG -Wl,-search_paths_first -Wl,-headerpad_max_install_names -static-intel -static-intel -openmp CMakeFiles/Anemone.dir/AnemoneMain.cxx.o  -o Anemone  
-L/usr/bin/icc-15.0-base/compiler/lib  
-L/usr/bin/ifort-15.0-base/compiler/lib  
/path/to/hdf5-1.8.6_intel-15.0_osx-10.9/lib/libhdf5_cpp.a 
/path/to/hdf5-1.8.6_intel-15.0_osx-10.9/lib/libhdf5.a 
libSomethingLib.a 
libSomethingElseLib.a 
libSomethingOrOtherLib.a 
/path/to/yaml-cpp-0.5.1_intel-15.0_osx-10.9/lib/libyaml-cpp.a 
/path/to/lapack-3.5.0_intel-15.0_osx-10.9/lib/libblas.a 
/path/to/lapack-3.5.0_intel-15.0_osx-10.9/lib/liblapack.a 
/path/to/lapack-3.5.0_intel-15.0_osx-10.9/lib/liblapacke.a 
/opt/intel/composer_xe_2015.1.108/mkl/lib/libmkl_intel_lp64.a 
/opt/intel/composer_xe_2015.1.108/mkl/lib/libmkl_core.a 
/opt/intel/composer_xe_2015.1.108/mkl/lib/libmkl_intel_thread.a 
-ldl 
/usr/lib/libz.dylib 
libSomethingLib.a 
/path/to/hdf5-1.8.6_intel-15.0_osx-10.9/lib/libhdf5_cpp.a 
/path/to/hdf5-1.8.6_intel-15.0_osx-10.9/lib/libhdf5.a 
/path/to/boost-1.57.0_intel-15.0_osx-10.9/lib/libboost_system.a 
/path/to/boost-1.57.0_intel-15.0_osx-10.9/lib/libboost_filesystem.a 
/path/to/boost-1.57.0_intel-15.0_osx-10.9/lib/libboost_timer.a 
/path/to/boost-1.57.0_intel-15.0_osx-10.9/lib/libboost_chrono.a 
-ldl 
/path/to/lapack-3.5.0_intel-15.0_osx-10.9/lib/libtmglib.a 
/path/to/lapack-3.5.0_intel-15.0_osx-10.9/lib/liblapack.a 
/path/to/lapack-3.5.0_intel-15.0_osx-10.9/lib/libblas.a 
-lm 
/usr/bin/icc-15.0-base/compiler/lib/libimf.a 
/usr/bin/icc-15.0-base/compiler/lib/libsvml.a 
/usr/bin/icc-15.0-base/compiler/lib/libirng.a 
/usr/bin/icc-15.0-base/compiler/lib/libipgo.a 
/usr/bin/icc-15.0-base/compiler/lib/libdecimal.a 
/usr/bin/icc-15.0-base/compiler/lib/libirc.a 
/usr/bin/icc-15.0-base/compiler/lib/libsvml.a 
/usr/bin/ifort-15.0-base/compiler/lib/libifport.a 
/usr/bin/ifort-15.0-base/compiler/lib/libifcore.a 
/usr/bin/ifort-15.0-base/compiler/lib/libimf.a 
/usr/bin/ifort-15.0-base/compiler/lib/libsvml.a 
/usr/bin/ifort-15.0-base/compiler/lib/libipgo.a 
/usr/bin/ifort-15.0-base/compiler/lib/libirc.a 
-lpthread 
/usr/bin/ifort-15.0-base/compiler/lib/libsvml.a

The version of the Intel compiler I am using is shown below.

$ icpc -V
Intel(R) C++ Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 15.0.2.132 Build 20150121

I am building this on a MacBookPro11,3 system running Apple OS X 10.9.5.

Thank you for any assistance you can provide with this.

Kind regards,

Anthony

0 Kudos
9 Replies
Feilong_H_Intel
Employee
159 Views

Hi Anthony,

I did a google search with keywords "ld: warning: can't find atom for N_GSYM stabs".  It shows several threads talking about this error.  In those threads, people were using GNU compiler and got similar warnings.  So, these warnings are probably related to something other than Intel compilers.  I'll continue the investigation and see if I will have more findings.

Thanks.

chinhster
Beginner
159 Views

I have the same problem with OS X 10.10. Everything was just fine prior to and including icc 15.0.1 and Xcode 6.2 (and earlier). I upgraded to Xcode 6.3 and icc 15.0.2 and started getting:

/ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal9FreeBlock12minBlockSizeE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
/ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal13BackRefMaster6dataSzE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
/ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal5Block16emptyEnoughRatioE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
/ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal18minLargeObjectSizeE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
/ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal10MemoryPool18defaultGranularityE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
/ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector10autoObjPtrE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
/ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector12owner_threadE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
/ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal9hugePagesE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
/ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector9rmc_mutexE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
/ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector23mallocRecursionDetectedE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
/ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal10MemoryPool15memPoolListLockE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)

 

However, my code also will no longer link with this error:

Assertion failed: (linked_addr_pos != line_table_map.end()), function FixReferences, file /SourceCache/dwarf_utilities/dwarf_utilities-121/source/DWARFdSYM.cpp, line 3883.
warning: {0x00018683} TAG_formal_parameter:  AT_location( 0xa1130000 ) didn't have valid function low pc, the location list will be incorrect.
Command /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/dsymutil failed with exit code 6

Once icc 15.0.3 came out, I upgraded to both Xcode 6.3.1 and icc 15.0.3 and still got the same warnings and error.

 

My Xcode project builds both a Cocoa GUI version of my app as well as a command-line version of my app. I can also build just the command-line version of my app without using Xcode using a makefile.  When I use the makefile, the console version builds just fine. It's only when I use Xcode and the recent versions of icc to build my app. There's no problem when I use Xcode 6.3.* and earlier with icc 15.0.1. I'm able to use icc 15.0.1 with Xcode 6.3.* by copying the 6.2 plugins directory to a 6.3 plugins directory. I can't recall if I tried icc 15.0.2 with Xcode 6.2 but I suspect I would've gotten the same result.

So in summary, Xcode 6.3 (and earlier) and icc 15.0.1 works builds my projects just fine. Xcode 6.3 and 15.0.2 or newer fails to build my projects.

Feilong_H_Intel
Employee
159 Views

Please note that, we started to support Xcode 6.3 from icc 15.0.3.  Could you please upgrade to icc 15.0.3 and see if the problem still persists.

Thanks.

Anthony_A_1
Beginner
159 Views

Greetings:

The same issue persists even with updated tools. Please see my output below for additional information.

ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal9FreeBlock12minBlockSizeE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal13BackRefMaster6dataSzE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal5Block16emptyEnoughRatioE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal18minLargeObjectSizeE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal10MemoryPool18defaultGranularityE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector10autoObjPtrE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector12owner_threadE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal9hugePagesE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector9rmc_mutexE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector23mallocRecursionDetectedE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal10MemoryPool15memPoolListLockE in /usr/bin/icpc-15.0-base/compiler/lib/libiomp5.a(iomp.o)

$ which icpc
/usr/bin/icpc

$ icpc -v
icpc version 15.0.3 (gcc version 5.1.0 compatibility)

$ xcodebuild -version
Xcode 6.3.1
Build version 6D1002

Thank you for your help with this.

Kind regards,

Anthony

chinhster
Beginner
159 Views

Has there been any progress made with this? We're pretty much stuck on Xcode 6.2 because of this bug in icc. 

Feilong_H_Intel
Employee
159 Views

I've entered this issue to our problem-tracking database.  The compiler library team will look into it.  I'll let you know once I get an update from them.

Thanks.

chinhster
Beginner
159 Views

What's the latest on this bug?

 

chinhster
Beginner
159 Views

m_ccompxe_2016.0.033 seems to have fixed the problem. However, I generate dSYM files so that I can symbolize crash logs from users later. I now get these warnings from within Xcode 6.4:

 

(null): warning: (x86_64) /nfs/fx/proj/openmp/promo/20150609/tmp/mac_32e-rtl_5_nor_sta.rel.41.r1.c0.s0...-fxeomac08/libtbbmalloc/backend.o unable to open object file: No such file or directory

(null): warning: (x86_64) /nfs/fx/proj/openmp/promo/20150609/tmp/mac_32e-rtl_5_nor_sta.rel.41.r1.c0.s0...-fxeomac08/libtbbmalloc/backref.o unable to open object file: No such file or directory

(null): warning: (x86_64) /nfs/fx/proj/openmp/promo/20150609/tmp/mac_32e-rtl_5_nor_sta.rel.41.r1.c0.s0...-fxeomac08/libtbbmalloc/frontend.o unable to open object file: No such file or directory

(null): warning: (x86_64) /nfs/fx/proj/openmp/promo/20150609/tmp/mac_32e-rtl_5_nor_sta.rel.41.r1.c0.s0...-fxeomac08/libtbbmalloc/large_objects.o unable to open object file: No such file or directory

(null): warning: (x86_64) /nfs/fx/proj/openmp/promo/20150609/tmp/mac_32e-rtl_5_nor_sta.rel.41.r1.c0.s0...-fxeomac08/libtbbmalloc/tbbmalloc.o unable to open object file: No such file or directory

 

But this is better than the previous problem which was failed compiles.

 

Sukruth_H_Intel
Employee
159 Views

Hi,

    I could see that one of the reason for the above issue may be to link the libraries statically : -

macmini01:shv root# ls
a.out           simple.cpp

macmini01:shv root# cat simple.cpp

#include<iostream>
#include<omp.h>
using namespace std;

int main()
{

        int a[20],b[20],c[20],i;

        for(i=0;i<20;i++)
        {
                a=b=i;
        }

        #pragma omp parallel for
        for(i=0;i<20;i++)
        {
                c=a+b;
                cout<<"Omp threads "<<omp_get_num_threads()<<endl;
        }

        cout<<"End element is "<<c[19]<<endl;

        return 0;
}

macmini01:shv root# icpc simple.cpp -openmp -static-intel

ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal9FreeBlock12minBlockSizeE in /opt/intel/composer_xe_2015.3.187/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal13BackRefMaster6dataSzE in /opt/intel/composer_xe_2015.3.187/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal5Block16emptyEnoughRatioE in /opt/intel/composer_xe_2015.3.187/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal18minLargeObjectSizeE in /opt/intel/composer_xe_2015.3.187/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal10MemoryPool18defaultGranularityE in /opt/intel/composer_xe_2015.3.187/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector10autoObjPtrE in /opt/intel/composer_xe_2015.3.187/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector12owner_threadE in /opt/intel/composer_xe_2015.3.187/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal9hugePagesE in /opt/intel/composer_xe_2015.3.187/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector9rmc_mutexE in /opt/intel/composer_xe_2015.3.187/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal28RecursiveMallocCallProtector23mallocRecursionDetectedE in /opt/intel/composer_xe_2015.3.187/compiler/lib/libiomp5.a(iomp.o)
ld: warning: can't find atom for N_GSYM stabs __ZN3rml8internal10MemoryPool15memPoolListLockE in /opt/intel/composer_xe_2015.3.187/compiler/lib/libiomp5.a(iomp.o)

macmini01:shv root# otool -L ./a.out

./a.out:
        /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)

macmini01:shv root# icpc simple.cpp -openmp

However from the issue that Feilong had raised for the engg team, they have now informed us that the issue is fixed in 16.0 compiler, Please do check and let us know if you need any further help from our side.

Regards,
Sukruth H V 

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