AMBER Archive (2008)

Subject: AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support

From: Pablo Englebienne (pablo.englebienne_at_mcgill.ca)
Date: Wed Sep 24 2008 - 14:04:46 CDT

I'm trying to compile PMEMD from Amber10 (fully patched) on an
InfiniBand-connected cluster of Pentium4 Xeon nodes (Mammouth-Mp @
RQCHP, if anyone has experience on it), but with little luck.

The short question is: how can I find where are the "Infiniband
libraries" required for compilation of PMEMD?

This is the walkthrough of what I did:

Based on the info on the README file, this is the output of 'mpif77
-link_info':
[englebie_at_ip05 pmemd]$ mpif77 -link_info
ifort -fPIC -L/opt/ofed/1.2.5.5/lib64 -D__INTEL_COMPILER -Wl,-rpath-link
-Wl,/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/shared
-L/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/shared
-L/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib -lmpichfarg -lmpich
-L/opt/ofed/1.2.5.5/lib64 -libverbs -libumad -libcommon -lpthread
-D__INTEL_COMPILER -lpthread -lrt

This is the command I'm using to configure the compilation:
[englebie_at_ip05 pmemd]$ ./configure linux_em64t ifort mvapich
Intel ifort compiler found; version information:
Version 10.1
configure assumes Intel MKL is installed in /opt/intel/mkl/10.0.3.020
File config_data/fft.pubfft being used...
File config_data/linux_em64t.ifort being used...
File config_data/interconnect.mvapich being used...
Please enter directory where mvapich mpi files are installed:
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9
Please enter name of directory where Infiniband libraries are installed:
/opt/ofed/1.2.5.5
PMEMD Configurate successfully completed.

When compiling, there is a long list of errors like the following ones:
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(waitall.o): In
function
 `MPI_Waitall':
(.text+0x8f): undefined reference to `MPID_SendComplete'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(waitall.o): In
function
 `MPI_Waitall':
(.text+0x128): undefined reference to `MPID_SendComplete'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(waitany.o): In
function
 `MPI_Waitany':
(.text+0x131): undefined reference to `MPID_SendIcomplete'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(waitany.o): In
function
 `MPI_Waitany':
(.text+0x383): undefined reference to `MPID_SendIcomplete'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Finalize':
(.text+0x362): undefined reference to `ibv_dereg_mr'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Finalize':
(.text+0x384): undefined reference to `ibv_dereg_mr'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Finalize':
(.text+0x475): undefined reference to `ibv_destroy_qp'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Finalize':
(.text+0x520): undefined reference to `ibv_destroy_qp'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Finalize':
(.text+0x607): undefined reference to `ibv_destroy_srq'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Finalize':
(.text+0x622): undefined reference to `ibv_destroy_cq'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Finalize':
(.text+0x650): undefined reference to `ibv_destroy_comp_channel'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Finalize':
(.text+0x719): undefined reference to `ibv_dealloc_pd'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Finalize':
(.text+0x734): undefined reference to `ibv_close_device'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x1a53): undefined reference to `ibv_get_device_list'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x1ac2): undefined reference to `ibv_get_device_name'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x1aee): undefined reference to `ibv_open_device'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x1b31): undefined reference to `ibv_query_port'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x1b43): undefined reference to `ibv_query_port'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x1b9e): undefined reference to `ibv_close_device'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x1c29): undefined reference to `ibv_open_device'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x1c53): undefined reference to `ibv_query_device'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x1c6e): undefined reference to `ibv_alloc_pd'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x1cb7): undefined reference to `ibv_query_port'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x1d8e): undefined reference to `ibv_free_device_list'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x2246): undefined reference to `ibv_query_device'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x2283): undefined reference to `ibv_query_pkey'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x2de1): undefined reference to `ibv_modify_srq'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x3407): undefined reference to `ibv_modify_qp'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x351c): undefined reference to `ibv_modify_qp'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `MPID_VIA_Init':
(.text+0x39be): undefined reference to `ibv_modify_srq'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `ib_init':
(.text+0x4eb6): undefined reference to `ibv_create_comp_channel'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `ib_init':
(.text+0x4ef2): undefined reference to `ibv_create_cq'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `ib_init':
(.text+0x4f44): undefined reference to `ibv_create_cq'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `ib_init':
(.text+0x4fe0): undefined reference to `ibv_create_srq'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `ib_init':
(.text+0x510e): undefined reference to `ibv_create_qp'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `ib_init':
(.text+0x51d4): undefined reference to `ibv_query_device'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `ib_init':
(.text+0x521e): undefined reference to `ibv_query_pkey'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viainit.o): In
function
 `ib_init':
(.text+0x5352): undefined reference to `ibv_modify_qp'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viacheck.o): In
functio
n `async_thread':
(.text+0x40): undefined reference to `ibv_get_async_event'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viacheck.o): In
functio
n `async_thread':
(.text+0x223): undefined reference to `ibv_modify_srq'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viacheck.o): In
functio
n `async_thread':
(.text+0x32d): undefined reference to `ibv_ack_async_event'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viacheck.o): In
function `MPID_DeviceCheck':
(.text+0x482): undefined reference to `odu_test_new_connection'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viacheck.o): In
functio
n `MPID_DeviceCheck':
(.text+0x663): undefined reference to `odu_test_new_connection'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viacheck.o): In
functio
n `MPID_DeviceCheck':
(.text+0x703): undefined reference to `ibv_get_cq_event'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viacheck.o): In
functio
n `MPID_DeviceCheck':
(.text+0x740): undefined reference to `ibv_ack_cq_events'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viacheck.o): In
functio
n `MPID_DeviceCheck':
(.text+0xbe4): undefined reference to `cm_process_queue'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viacheck.o): In
functio
n `MPID_DeviceCheck':
(.text+0xfe2): undefined reference to `cm_process_queue'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viapriv.o): In
function
 `viadev_ext_sendq_send':
(.text+0x155): undefined reference to `prepare_coalesced_pkt'
/opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9/lib/libmpich.a(viapriv.o): In
function
 `deregister_memory':
(.text+0x15c6): undefined reference to `ibv_dereg_mr'

Any suggestions? 

-- 
Pablo Englebienne, PhD Student, Moitessier research group
Department of Chemistry, McGill University
801 Sherbrooke Street West
Otto Maass bldg, room 206
H3A 2K6 Montréal, Québec, Canada
Tel (514) 398-5501    Fax (514) 398-2382

"Progress is made by lazy men looking for easier ways to do things." - Robert A. Heinlein

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