AMBER Archive (2006)

Subject: Re: AMBER: pmemd installation problem

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Nov 03 2006 - 13:09:52 CST

Looks to me like you are missing a library for mvapich. Try entering a
"mpif77 -link_info", assuming the correct mpi implementation is in your
path. If you do have the right libraries, then they may not have been built
with a pgi-compatible compiler, so you then have name mangling issues.
Other than the possibility of an outdated pgi compiler (somewhere pre-6.0
they had bugs that screwed up pmemd), I thought I had configuration working
pretty well for pgi, but it is not like I run this stuff everywhere. I
would think if you are actually building a runnable mpi version of sander,
you could look at the config script for that and figure out which library
you are missing for pmemd (the fact you say you are building parallel sander
makes me think it is most likely you are just missing a critical library in
the ld).
Regards - Bob Duke

----- Original Message -----
From: "Ed Pate" <pate_at_math.wsu.edu>
To: <amber_at_scripps.edu>
Sent: Friday, November 03, 2006 1:51 PM
Subject: AMBER: pmemd installation problem

> Dear Amber community:
>
> We are trying to install Amber 8 on an Opteron 275-based system system
> using SUSE 10.0 and the Portland Group compilers. We are using the
> instructions downloaded from the PG website,
> http://www.pgroup.com/resources/amber/amber8_pgi60.htm.
>
> This requires downloading two new configure files for sander and pmemd, 4
> files to go in pmemd/config_data, and modifying a line of code in
> /amber8/src/leap/Makefile.
>
> The 64-bit serial installation and the parallel installation for sander
> appear to go OK.
>
> The installation of pmemd is not working. Can anyone help me to see what
> I need to do?
>
> Thanks,
>
> Ed Pate
>
> The job script and output for the pmemd installation follows:
>
> beowulf src/pmemd> ./configure_pmemd linux_opteron pgf90 mpich
> PMEMD is assuming MPICH files are installed in /usr/local/mvapich.
>
> beowulf src/pmemd> make install
>
> make[1]: Entering directory `/home/pate/amber8.d/amber8/src/pmemd/src'
> ../Compile LOAD -o pmemd gbl_constants.o gbl_datatypes.o file_io_dat.o
> parallel_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o
> gbl_dat.o ew_dat.o ew_direct_cit_dat.o ew_direct_cit.o ew_recip_cit.o
> ew_fft_cit.o ew_force_cit.o ew_bspline.o ew_box.o ew_pairlist.o
> force_cit.o runmd_cit.o shake_cit.o runmin_cit.o axis_optimize_cit.o
> ew_lib.o pmemd_lib.o runfiles.o file_io.o pmemd_clib.o pmemd.o random.o
> degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o
> alltasks_setup.o ew_setup.o nextprmtop_section.o
> pgf90 -fastsse -Mipa=fast -o pmemd gbl_constants.o gbl_datatypes.o
> file_io_dat.o parallel_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o
> inpcrd_dat.o gbl_dat.o ew_dat.o ew_direct_cit_dat.o ew_direct_cit.o
> ew_recip_cit.o ew_fft_cit.o ew_force_cit.o ew_bspline.o ew_box.o
> ew_pairlist.o force_cit.o runmd_cit.o shake_cit.o runmin_cit.o
> axis_optimize_cit.o ew_lib.o pmemd_lib.o runfiles.o file_io.o pmemd_clib.o
> pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o
> master_setup.o alltasks_setup.o ew_setup.o
> nextprmtop_section.o -L/usr/local//usr/local/mvapich/lib/libmpich.a(viainit.o):
> In function `open_hca':
> viainit.c:(.text+0x141): undefined reference to `ibv_get_device_list'
> viainit.c:(.text+0x185): undefined reference to `ibv_get_device_name'
> viainit.c:(.text+0x1e7): undefined reference to `ibv_open_device'
> viainit.c:(.text+0x1f6): undefined reference to `ibv_free_device_list'
> viainit.c:(.text+0x264): undefined reference to `ibv_alloc_pd'
> /usr/local/mvapich/lib/libmpich.a(viainit.o): In function `get_lid':
> viainit.c:(.text+0x31f): undefined reference to `ibv_query_port'
> viainit.c:(.text+0x373): undefined reference to `ibv_query_port'
> /usr/local/mvapich/lib/libmpich.a(viainit.o): In function `create_cq':
> viainit.c:(.text+0x412): undefined reference to `ibv_create_cq'
> /usr/local/mvapich/lib/libmpich.a(viainit.o): In function `create_srq':
> viainit.c:(.text+0x4cc): undefined reference to `ibv_create_srq'
> /usr/local/mvapich/lib/libmpich.a(viainit.o): In function `ib_init':
> viainit.c:(.text+0xbe1): undefined reference to `ibv_create_qp'
> viainit.c:(.text+0xcc4): undefined reference to `ibv_modify_qp'
> /usr/local/mvapich/lib/libmpich.a(viainit.o): In function `ib_qp_enable':
> viainit.c:(.text+0xe3a): undefined reference to `ibv_modify_qp'
> viainit.c:(.text+0xf41): undefined reference to `ibv_modify_qp'
> viainit.c:(.text+0x10d7): undefined reference to `pthread_spin_init'
> viainit.c:(.text+0x10e1): undefined reference to
> `pthread_spin_lock'mvapich/lib -lmpich
> IPA: no IPA optimizations for 8 source files
> IPA: IPA information unchanged for 28 source files
> /usr/local/mvapich/lib/libmpich.a(viainit.o): In function `open_hca':
> viainit.c:(.text+0x141): undefined reference to `ibv_get_device_list'
> viainit.c:(.text+0x185): undefined reference to `ibv_get_device_name'
> viainit.c:(.text+0x1e7): undefined reference to `ibv_open_device'
> viainit.c:(.text+0x1f6): undefined reference to `ibv_free_device_list'
> viainit.c:(.text+0x264): undefined reference to `ibv_alloc_pd'
> /usr/local/mvapich/lib/libmpich.a(viainit.o): In function `get_lid':
> viainit.c:(.text+0x31f): undefined reference to `ibv_query_port'
> viainit.c:(.text+0x373): undefined reference to `ibv_query_port'
> /usr/local/mvapich/lib/libmpich.a(viainit.o): In function `create_cq':
> viainit.c:(.text+0x412): undefined reference to `ibv_create_cq'
> /usr/local/mvapich/lib/libmpich.a(viainit.o): In function `create_srq':
> viainit.c:(.text+0x4cc): undefined reference to `ibv_create_srq'
>
> ************this type of message continues*********************
>
> /usr/local/mvapich/lib/libmpich.a(viarecv.o): In function
> `viadev_recv_r3':
> viarecv.c:(.text+0x3e6): undefined reference to `pthread_spin_lock'
> viarecv.c:(.text+0x40c): undefined reference to `pthread_spin_unlock'
> child process exit status 1: /usr/bin/ld
> make[1]: *** [pmemd] Error 1
> make[1]: Leaving directory `/home/pate/amber8.d/amber8/src/pmemd/src'
> make: *** [install] Error 2
>
>
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