Re: [gmx-users] please help, cannot compile gmx 4.5 openmm

[Alan]

Dear Rossen,

Thanks for your reply.

For your info I use Mac 10.6 with Fink in 64 bits. I have access to svn
Openmm dev source code so I am compiling it in 64 bits. It could be a source
of issues, but all others programmes I have running that depends on openmm
(e.g. sander_openmm) were working fine except GMX.

Bizzarely but gmx 4.5 beta were compiling ok.

I will try release-4-5-patches updated later.

Thanks,

Alan

On 13 September 2010 12:58, Rossen Apostolov  wrote:

>  Just to add: the pre-built OpenMM-2.0 for Mac are compiled for 32bit. If
> you get an error as:
>
> Linking CXX shared library libopenmm_api_wrapper.dylib
> ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was built for
> i386 which is not the architecture being linked (x86_64)
> Undefined symbols:
>   "OpenMM::State::getVelocities() const", referenced from:
>  snip .
>
> then you can force compilation for 32bit by:
>
> $ export CFLAGS='-arch i386'
> $ export CXXFLAGS='-arch i386'
>
> or recompile the openmm from source.
>
> Rossen
>
>
> On 9/13/10 1:01 PM, Rossen Apostolov wrote:
>
> Hi Alan,
>
> There was a missing dependency for building gmx_gpu_utils, but for some
> reason compilation didn't break on linux:) This is now fixed in
> release-4-5-patches. Pay attention though that the prebuilt  OpenMM-2.0
> libraries from the SimTK website are for MacOSX 10.6
>
> Rossen
>
> On 9/11/10 12:56 AM, Alan wrote:
>
> I am doing, after compiling and installing the normal grmx 4.5:
>
>  rm -fr CMakeCache.txt
> make clean
> export OPENMM_ROOT_DIR=/usr/local/openmm
>  cmake -DGMX_OPENMM=ON ..
> make mdrun
>  [  1%] Building NVCC (Device) object
> src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o
> [  1%] Building NVCC (Device) object
> src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
> Scanning dependencies of target gmx_gpu_utils
> Linking CXX shared library libgmx_gpu_utils.dylib
> Undefined symbols:
>   "_gmx_strncasecmp", referenced from:
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   "_debug", referenced from:
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   do_timed_memtest(int, int)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   do_full_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   do_quick_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   "_trim", referenced from:
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
> make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1
> make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all]
> Error 2
> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
> make: *** [mdrun] Error 2
>
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <<
>
>
>
> --
> -Rossen
>
>
>
> --
> -Rossen
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.u

Re: [gmx-users] please help, cannot compile gmx 4.5 openmm

[Rossen Apostolov]

 Just to add: the pre-built OpenMM-2.0 for Mac are compiled for 32bit. 
If you get an error as:


Linking CXX shared library libopenmm_api_wrapper.dylib
ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was built 
for i386 which is not the architecture being linked (x86_64)

Undefined symbols:
  "OpenMM::State::getVelocities() const", referenced from:
 snip .

then you can force compilation for 32bit by:

$ export CFLAGS='-arch i386'
$ export CXXFLAGS='-arch i386'

or recompile the openmm from source.

Rossen

On 9/13/10 1:01 PM, Rossen Apostolov wrote:

Hi Alan,

There was a missing dependency for building gmx_gpu_utils, but for 
some reason compilation didn't break on linux:) This is now fixed in 
release-4-5-patches. Pay attention though that the prebuilt  
OpenMM-2.0 libraries from the SimTK website are for MacOSX 10.6


Rossen

On 9/11/10 12:56 AM, Alan wrote:

I am doing, after compiling and installing the normal grmx 4.5:

rm -fr CMakeCache.txt
make clean
export OPENMM_ROOT_DIR=/usr/local/openmm
cmake -DGMX_OPENMM=ON ..
make mdrun
[  1%] Building NVCC (Device) object 
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o
[  1%] Building NVCC (Device) object 
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

Scanning dependencies of target gmx_gpu_utils
Linking CXX shared library libgmx_gpu_utils.dylib
Undefined symbols:
  "_gmx_strncasecmp", referenced from:
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

  "_debug", referenced from:
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  do_timed_memtest(int, int)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

  do_full_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  do_quick_memtest(int)  in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

  "_trim", referenced from:
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

ld: symbol(s) not found
collect2: ld returned 1 exit status
make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1
make[2]: *** 
[src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2

make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
make: *** [mdrun] Error 2



--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28 <<



--
-Rossen



--
-Rossen

-- 
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Re: [gmx-users] please help, cannot compile gmx 4.5 openmm

[Rossen Apostolov]

 Hi Alan,

There was a missing dependency for building gmx_gpu_utils, but for some 
reason compilation didn't break on linux:) This is now fixed in 
release-4-5-patches. Pay attention though that the prebuilt  OpenMM-2.0 
libraries from the SimTK website are for MacOSX 10.6


Rossen

On 9/11/10 12:56 AM, Alan wrote:

I am doing, after compiling and installing the normal grmx 4.5:

rm -fr CMakeCache.txt
make clean
export OPENMM_ROOT_DIR=/usr/local/openmm
cmake -DGMX_OPENMM=ON ..
make mdrun
[  1%] Building NVCC (Device) object 
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o
[  1%] Building NVCC (Device) object 
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

Scanning dependencies of target gmx_gpu_utils
Linking CXX shared library libgmx_gpu_utils.dylib
Undefined symbols:
  "_gmx_strncasecmp", referenced from:
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

  "_debug", referenced from:
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  do_timed_memtest(int, int)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

  do_full_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  do_quick_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  "_trim", referenced from:
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
  is_supported_cuda_gpu(int, char*)in 
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o

ld: symbol(s) not found
collect2: ld returned 1 exit status
make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1
make[2]: *** 
[src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2

make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
make: *** [mdrun] Error 2



--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28 <<



--
-Rossen

-- 
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Re: [gmx-users] please help, cannot compile gmx 4.5 openmm

[Szilárd Páll]

Hi Alan,

I assume this is still the same issue on the same issue (same
machine/os) as you reported last time.

Could you provide some details about the version of OS, compiler,
CUDA, OpenMM you're using?

I'll look into the problem and get back to you if I figure out something.

Cheers,
--
Szilárd



On Sat, Sep 11, 2010 at 12:56 AM, Alan  wrote:
> I am doing, after compiling and installing the normal grmx 4.5:
> rm -fr CMakeCache.txt
> make clean
> export OPENMM_ROOT_DIR=/usr/local/openmm
> cmake -DGMX_OPENMM=ON ..
> make mdrun
> [  1%] Building NVCC (Device) object
> src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o
> [  1%] Building NVCC (Device) object
> src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
> Scanning dependencies of target gmx_gpu_utils
> Linking CXX shared library libgmx_gpu_utils.dylib
> Undefined symbols:
>   "_gmx_strncasecmp", referenced from:
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   "_debug", referenced from:
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       do_timed_memtest(int, int)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       do_full_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       do_quick_memtest(int)  in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>   "_trim", referenced from:
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
>       is_supported_cuda_gpu(int, char*)in
> gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
> make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1
> make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all]
> Error 2
> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
> make: *** [mdrun] Error 2
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>>http://www.bio.cam.ac.uk/~awd28<<
>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
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Please search the archive at 
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