Hi,
On Tue, Sep 3, 2019 at 3:34 AM xmgign.126.com <xmgign.126.com> wrote:
> /public/home/test/amber18/lib/libfftw3.a(vrank3-transpose.o): In function `apply_cut':
> vrank3-transpose.c:(.text+0x5f7): undefined reference to `_intel_fast_memmove'
This indicates that libfftw3.a was compiled with intel compilers. It
needs to be recompiled if you are switching to gnu compilers. Remove
this file and try to build again. To be completely safe you may want
to remove all libfftw* files from $AMBERHOME/lib and then re-run
configure.
-Dan
> vrank3-transpose.c:(.text+0x661): undefined reference to `_intel_fast_memcpy'
> vrank3-transpose.c:(.text+0x6b9): undefined reference to `_intel_fast_memcpy'
> vrank3-transpose.c:(.text+0x748): undefined reference to `_intel_fast_memmove'
> vrank3-transpose.c:(.text+0x803): undefined reference to `_intel_fast_memcpy'
> /public/home/test/amber18/lib/libfftw3.a(vrank3-transpose.o): In function `apply_toms513':
> vrank3-transpose.c:(.text+0xf10): undefined reference to `_intel_fast_memset'
> vrank3-transpose.c:(.text+0x1017): undefined reference to `_intel_fast_memcpy'
> vrank3-transpose.c:(.text+0x1037): undefined reference to `_intel_fast_memcpy'
> vrank3-transpose.c:(.text+0x1151): undefined reference to `_intel_fast_memcpy'
> vrank3-transpose.c:(.text+0x117b): undefined reference to `_intel_fast_memcpy'
> vrank3-transpose.c:(.text+0x120c): undefined reference to `_intel_fast_memcpy'
> /public/home/test/amber18/lib/libfftw3.a(vrank3-transpose.o):vrank3-transpose.c:(.text+0x1227): more undefined references to `_intel_fast_memcpy' follow
> collect2: error: ld returned 1 exit status
> make[2]: *** [/public/home/test/amber18/bin/sander] Error 1
> make[2]: Leaving directory `/public/home/test/amber18/AmberTools/src/sander'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory `/public/home/test/amber18/AmberTools/src'
> make: *** [install] Error 2
>
> I do not find any useful information from internet, what should I do to solve the problem ?
>
>
> The intel compiler also has problem
> Based on the intel compiler, I have installed AMBER18 successfully.
> But it failed to work. I tested the MMPBSA.py.MPI
> and the errors:
>
>
> "ibv_exp_query_device: invalid comp_mask !!! (comp_mask = 0xffffffffffffffff valid_mask = 0x3)
> [comput10][[9043,1],0][btl_openib_component.c:1648:init_one_device] error obtaining device attributes for mlx4_0 errno says Invalid argument
> ibv_exp_query_device: invalid comp_mask !!! (comp_mask = 0xffffffffffffffff valid_mask = 0x3)
> [comput10][[9043,1],2][btl_openib_component.c:1648:init_one_device] error obtaining device attributes for mlx4_0 errno says Invalid argument
> ibv_exp_query_device: invalid comp_mask !!! (comp_mask = 0xffffffffffffffff valid_mask = 0x3)
> [comput10][[9043,1],3][btl_openib_component.c:1648:init_one_device] error obtaining device attributes for mlx4_0 errno says Invalid argument
> ibv_exp_query_device: invalid comp_mask !!! (comp_mask = 0xffffffffffffffff valid_mask = 0x3)
> [comput10][[9043,1],1][btl_openib_component.c:1648:init_one_device] error obtaining device attributes for mlx4_0 errno says Invalid argument
> /public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
> warn('Solvated topology %s has IFBOX == 0' % ifbox)
> [comput10:32028] 3 more processes have sent help message help-mpi-btl-openib.txt / error in device init
> [comput10:32028] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
> forrtl: severe (168): Program Exception - illegal instruction
> Image PC Routine Line Source
> libifcoremt.so.5 00002B052A7D8575 for__signal_handl Unknown Unknown
> libpthread-2.17.s 00002B052B57F5D0 Unknown Unknown Unknown
> sander 000000000060A060 init_timers_ Unknown Unknown
> sander 00000000004F4A09 sander_ Unknown Unknown
> sander 00000000004F48E2 MAIN__ Unknown Unknown
> sander 000000000046CAEE main Unknown Unknown
> libc-2.17.so 00002B052B7AE3D5 __libc_start_main Unknown Unknown
> sander 000000000046C9F9 Unknown Unknown Unknown
> forrtl: severe (168): Program Exception - illegal instruction
> Image PC Routine Line Source
> libifcoremt.so.5 00002B79AA6E2575 for__signal_handl Unknown Unknown
> libpthread-2.17.s 00002B79AB4895D0 Unknown Unknown Unknown
> sander 000000000060A060 init_timers_ Unknown Unknown
> sander 00000000004F4A09 sander_ Unknown Unknown
> sander 00000000004F48E2 MAIN__ Unknown Unknown
> sander 000000000046CAEE main Unknown Unknown
> Image PC Routine Line Source
> libifcoremt.so.5 00002AFA70111575 for__signal_handl Unknown Unknown
> libpthread-2.17.s 00002AFA70EB85D0 Unknown Unknown Unknown
> sander 000000000060A060 init_timers_ Unknown Unknown
> sander 00000000004F4A09 sander_ Unknown Unknown
> sander 00000000004F48E2 MAIN__ Unknown Unknown
> sander 000000000046CAEE main Unknown Unknown
> libc-2.17.so 00002AFA710E73D5 __libc_start_main Unknown Unknown
> sander 000000000046C9F9 Unknown Unknown Unknown
> forrtl: severe (168): Program Exception - illegal instruction
> Image PC Routine Line Source
> libifcoremt.so.5 00002AB59055A575 for__signal_handl Unknown Unknown
> libpthread-2.17.s 00002AB5913015D0 Unknown Unknown Unknown
> sander 000000000060A060 init_timers_ Unknown Unknown
> sander 00000000004F4A09 sander_ Unknown Unknown
> sander 00000000004F48E2 MAIN__ Unknown Unknown
> sander 000000000046CAEE main Unknown Unknown
> libc-2.17.so 00002AB5915303D5 __libc_start_main Unknown Unknown
> sander 000000000046C9F9 Unknown Unknown Unknown
> File "/public/home/test/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
> File "/public/home/test/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
> File "/public/home/test/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
> File "/public/home/test/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
> app.run_mmpbsa()
> File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
> app.run_mmpbsa()
> File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
> app.run_mmpbsa()
> File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
> app.run_mmpbsa()
> File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
> self.calc_list.run(rank, self.stdout)
> File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
> self.calc_list.run(rank, self.stdout)
> File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
> self.calc_list.run(rank, self.stdout)
> File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
> self.prmtop))
> self.prmtop))
> CalcError: /public/home/test/amber18/bin/sander failed with prmtop ../../../../07-topX3/gper1-g1.prmtop!
> CalcError: /public/home/test/amber18/bin/sander failed with prmtop ../../../../07-topX3/gper1-g1.prmtop!
> self.prmtop))
> self.prmtop))
> Error occured on rank 3.
> Exiting. All files have been retained.
> Error occured on rank 1.
> Exiting. All files have been retained.
> CalcError: /public/home/test/amber18/bin/sander failed with prmtop ../../../../07-topX3/gper1-g1.prmtop!
> CalcError: /public/home/test/amber18/bin/sander failed with prmtop ../../../../07-topX3/gper1-g1.prmtop!
> Error occured on rank 2.
> Exiting. All files have been retained.
> Error occured on rank 0.
> Exiting. All files have been retained.
> [comput10:32028] 3 more processes have sent help message help-mpi-api.txt / mpi-abort"
>
> The installation of Amber16 also have similar problems.
>
> The operating system is centos 7.6.
> I have yum gcc gcc-gfortran gcc-c++ flex tcsh zlib-devel \
> bzip2-devel libXt-devel libXext-devel libXdmcp-devel tkinter \
> openmpi perl perl-ExtUtils-MakeMaker patch bison
> the yum can not install openmpi-devel, thus I installed the openmpi based on gnu and intel compiler.
>
> So I am confused about what the problem is.
> Best regards
>
> Qiao Xue
>
>
>
> xmgign.126.com
> _______________________________________________
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Received on Tue Sep 03 2019 - 06:00:02 PDT
