Hi Filip and everyone,
Thanks for your suggestion. But the problem seem still to happen again. When I enter the command:"./patch_amber.py --update"
--------------------------------------------------------------------------------------------------------------------------------------------------
javacfish.linux-th8x:~/soft/amber12> ./patch_amber.py --update
Determining patches to download for AmberTools12
AmberTools12 is up to date. Nothing to download
Determining patches to download for Amber12
Amber12 is up to date. Nothing to download
---------------------------------------------------------------------------------------------------------------------------------------------------
I make sure all update completely. However, I run ./configure gnu, and then knock the command:"make install", the err happens as below:
********************************************************************************************
vrank3-transpose.c:(.text+0x1246): undefined reference to `__intel_ssse3_memcpy'
/home/bai/soft/amber12/lib/libfftw3.a(vrank3-transpose.o):vrank3-transpose.c:(.text+0x1261): more undefined references to `__intel_ssse3_memcpy' follow
/home/bai/soft/amber12/lib/libfftw3.a(trig.o): In function `cexpl_sincos':
trig.c:(.text+0x189): undefined reference to `__libm_sse2_sincos'
/home/bai/soft/amber12/lib/libfftw3.a(trig.o): In function `fftw_mktriggen':
trig.c:(.text+0x41e): undefined reference to `__libm_sse2_sincos'
trig.c:(.text+0x52e): undefined reference to `__libm_sse2_sincos'
collect2: error: ld returned 1 exit status
make[2]: *** [pbsa] Error 1
make[2]: Leaving directory `/home/bai/soft/amber12/AmberTools/src/pbsa'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/home/bai/soft/amber12/AmberTools/src'
make: *** [install] Error 2
********************************************************************************************
Could you give me more advice?
Thanks
Javacfish
________________________________
From: filip fratev <filipfratev.yahoo.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, March 14, 2013 6:44 AM
Subject: Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3
Solved. "the standard c++
library was linked by default... but maybe it's a CUDA compiler issue
..."
This was the issue. Start from suse 12 one should just add manually /usr/lib64/..
All the best,
Filip
________________________________
From: filip fratev <filipfratev.yahoo.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, March 13, 2013 11:55 PM
Subject: Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3
Hi all,
I have a problem to install the cuda version of Amber 12 on Opensuse 12.1,12.2 and 12.3. Currently, I downgraded to 12.1 to avoid any potential compiler issues on 12.2 and 12.3.
The same issue has been already discussed but not solved here:
http://archive.ambermd.org/201204/0738.html
I planed to post some test results using GTX Titan's, but I am not able to build pmemd.cuda..:(
Here is my output:
nbondEnergy1.o kNLRadixSort.o kCalculateGBNonbondEnergy2.o kShake.o kNeighborList.o kPMEInterpolation.o kCalculateAMDWeights.o
ar: creating cuda.a
a - cuda_info.o
a - gpu.o
a - gputypes.o
a - kForcesUpdate.o
a - kCalculateLocalForces.o
a - kCalculateGBBornRadii.o
a - kCalculatePMENonbondEnergy.o
a - kCalculateGBNonbondEnergy1.o
a - kNLRadixSort.o
a - kCalculateGBNonbondEnergy2.o
a - kShake.o
a - kNeighborList.o
a - kPMEInterpolation.o
a - kCalculateAMDWeights.o
make[5]: Leaving directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
gfortran -O3 -mtune=native -DCUDA -Duse_SPFP -o pmemd.cuda gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o nbips.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o pmemd_lib.o runfiles.o file_io.o bintraj.o binrestart.o pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o charmm.o charmm_gold.o findmask.o remd.o multipmemd.o
remd_exchg.o amd.o gbsa.o \
./cuda/cuda.a -L/usr/local/cuda-5.0/lib64 -L/usr/local/cuda-5.0/lib -lcurand -lcufft -lcudart -L/home/fratev-2/amber12/lib -L/home/fratev-2/amber12/lib -lnetcdf
/usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../x86_64-suse-linux/bin/ld: ./cuda/cuda.a(gpu.o): undefined reference to symbol 'operator new[](unsigned long)@@GLIBCXX_3.4'
/usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../x86_64-suse-linux/bin/ld: note: 'operator new[](unsigned long)@@GLIBCXX_3.4' is defined in DSO /usr/lib64/libstdc++.so.6 so try adding it to the linker command line
/usr/lib64/libstdc++.so.6: could not read symbols: Invalid operation
collect2: ld returned 1 exit status
make[4]: *** [pmemd.cuda] Error 1
make[4]: Leaving directory `/home/fratev-2/amber12/src/pmemd/src'
make[3]: *** [cuda] Error 2
make[3]: Leaving directory `/home/fratev-2/amber12/src/pmemd'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/home/fratev-2/amber12/src'
make[1]: [cuda] Error 2 (ignored)
make[1]: Leaving directory `/home/fratev-2/amber12/AmberTools/src'
make[1]: Entering directory `/home/fratev-2/amber12/src'
Starting installation of Amber12 (cuda) at ср мар 13 23:39:02 EET 2013.
cd pmemd && make cuda
make[2]: Entering directory `/home/fratev-2/amber12/src/pmemd'
make -C src/ cuda
make[3]: Entering directory `/home/fratev-2/amber12/src/pmemd/src'
make -C ./cuda
make[4]: Entering directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/home/fratev-2/amber12/src/pmemd/src/cuda'
gfortran -O3 -mtune=native -DCUDA -Duse_SPFP -o pmemd.cuda gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o nbips.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o pmemd_lib.o runfiles.o file_io.o bintraj.o binrestart.o pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o charmm.o charmm_gold.o findmask.o remd.o multipmemd.o
remd_exchg.o amd.o gbsa.o \
./cuda/cuda.a -L/usr/local/cuda-5.0/lib64 -L/usr/local/cuda-5.0/lib -lcurand -lcufft -lcudart -L/home/fratev-2/amber12/lib -L/home/fratev-2/amber12/lib -lnetcdf
/usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../x86_64-suse-linux/bin/ld: ./cuda/cuda.a(gpu.o): undefined reference to symbol 'operator new[](unsigned long)@@GLIBCXX_3.4'
/usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../x86_64-suse-linux/bin/ld: note: 'operator new[](unsigned long)@@GLIBCXX_3.4' is defined in DSO /usr/lib64/libstdc++.so.6 so try adding it to the linker command line
/usr/lib64/libstdc++.so.6: could not read symbols: Invalid operation
collect2: ld returned 1 exit status
make[3]: *** [pmemd.cuda] Error 1
make[3]: Leaving directory `/home/fratev-2/amber12/src/pmemd/src'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/home/fratev-2/amber12/src/pmemd'
make[1]: *** [cuda] Error 2
make[1]: Leaving directory `/home/fratev-2/amber12/src'
make: *** [install] Error 2
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: javacfish <javacfish.yahoo.com.cn>; AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, March 13, 2013 11:19 PM
Subject: Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3
This was fixed some time ago. Update your system first and then try again.
You can update Amber by doing:
cd $AMBERHOME
./patch_amber.py --update
Keep running ./patch_amber.py --update until it tells you that there are no
updates to apply. Then re-run configure and build Amber.
HTH,
Jason
On Wed, Mar 13, 2013 at 1:54 PM, javacfish <javacfish.yahoo.com.cn> wrote:
> Hello everyone,
>
> when I install Amber12 on the Opensuse linux (gcc version 4.7.1 20120723),
> I used ./configure gnu. But when I run make install, the err happen as
> below:
>
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------------
> a - mkl_fft.o
> ranlib /home/bai/soft/amber12/lib/librism.a
> gfortran -c -DBINTRAJ \
> \
> -O3 -mtune=native -ffree-form -I/home/bai/soft/amber12/include
> -I/home/bai/soft/amber12/include \
> -o rism1d.o rism1d.F90
> rism1d.F90:1262.8:
>
> use rism1d_m
> 1
> Error: 'rism1d' of module 'rism1d_m', imported at (1), is also the name of
> the current program unit
> rism1d.F90:1262.8:
>
> use rism1d_m
> 1
> Error: Name 'rism1d' at (1) is an ambiguous reference to 'rism1d' from
> current program unit
> rism1d.F90:1261.16:
>
> program rism1d
> 1
> Error: Name 'rism1d' at (1) is an ambiguous reference to 'rism1d' from
> current program unit
> make[2]: *** [rism1d.o] Error 1
> make[2]: Leaving directory `/home/bai/soft/amber12/AmberTools/src/rism'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory `/home/bai/soft/amber12/AmberTools/src'
> make: *** [install] Error 2
>
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------------
>
>
> Could someone help me? Give me some suggestion?
>
> Thanks
>
> javacfish
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Mar 14 2013 - 02:30:03 PDT
