AMBER Archive (2006)

Subject: AMBER: pmemd installation problem

From: Ed Pate (pate_at_math.wsu.edu)
Date: Fri Nov 03 2006 - 12:51:36 CST

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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