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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
Robert Duke wrote:
> Looks to me like you should modify config.h as follows:
>
> MPI_LIBDIR2 = /opt/ofed/1.2.5.5/lib64
> MPI_HOME = /opt/ofed/1.2.5.5/mpi/intel/mvapich-0.9.9
>
> modify the MPI_LIBS line to list the libraries -libverbs -libumad
> -libcommon -lpthread after -L(MPI_LIBDIR2)
> modify the MPI_LIBS line to list the libraries -lmpichfarg -lmpich
> after -L(MPI_LIBDIR)
>
> Alternatively, it may be most simple to use mpif77 in place of ifort
> in the config.h file, and drop all the MPI_LIB* stuff; I have
> typically not done this because I want to absolutely control what is
> happening, but if you find the correct mpif77 for your installation,
> and the installation has not been dinked with ("customized", perhaps
> not entirely correctly), that may prove simpler. I think Ross has
> released some more detailed directions on this option on the
> reflector; I may eventually give in and make this an easily available
> option in configure (there is a bunch of other stuff going on in the
> -link_info output here that you may or may not actually need; I
> typically have no way of knowing without access to the machine).
>
> Best regards - Bob Duke
>
> ----- Original Message ----- From: "Pablo Englebienne"
> <pablo.englebienne.mcgill.ca>
> To: <amber.scripps.edu>
> Sent: Wednesday, September 24, 2008 3:04 PM
> Subject: AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support
>
>
>> 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.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.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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>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo.scripps.edu
>>
>
> -----------------------------------------------------------------------
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> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
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Received on Fri Sep 26 2008 - 05:11:35 PDT