Dear Hornak:
Thank you very much for your response!
Yes, I did compile mpich with ifort. I'm also confused about it. I don't
know the output by "nm $MPICH_HOME/lib/libmpich.a". Would you please
check it for me? It's attached below. Many thanks!
Best!
Liu
Viktor Hornak wrote:
> Dear Liu,
>
> this looks like trailing underscore problem. Are you sure you compiled
> mpich with ifort?
> What does "nm $MPICH_HOME/lib/libmpich.a" output look like?
>
> -Viktor
>
> scopio wrote:
>
>> Dear Amber Users:
>>
>> I'm now compiling Amber7 on Redhat9 with ifc8.0 by following the
>> instruction at http://amber.scripps.edu/cluster_info/compile_a7.html.
>>
>> I installed ifc8.0 and then compiled mpich-1.2.5.2. All seem go well
>> before I go to amber7/src directory tring to compile amber.
>>
>> The machine file I use is downloaded from
>> http://amber.scripps.edu/cluster_info/Machine.ifort_mpich. And
>> bugfix.1 has been applied to amber7/src/lapack/Makefile. Next, I type
>> 'make install' after setenv $AMBERHOME and $MPICH_HOME. The problem
>> seems ocurred at the step compiling sander. Below are the error message:
>> ====
>> dtrsm.o dtrsv.o dummy.o dzasum.o dznrm2.o idamax.o isamax.o lsame.o
>> ../Compile RANLIB blas.a
>> ranlib blas.a
>> make[3]: Leaving directory `/home/liu/amber7/src/blas'
>> make[2]: Leaving directory `/home/liu/amber7/src/blas'
>> SYSLIB=`../sysdir lib` ; ../Compile LOAD -o sander \
>> sander.o cshf.o noecalc.o noeread.o caldis.o
>> calrate.o dinten.o drates.o indexn.o kmat.o pearsn.o plane.o remarc.o
>> nmrcal.o
>> ................
>> ................
>> ecomp.o ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o
>> /home/liu/amber7/src/Machines/standard/sys.a
>> -L/usr/local/mpich-1.2.5.2_icc/lib -lmpich -lpmpich
>> sander.o(.text+0x50): In function `MAIN__':
>> : undefined reference to `mpi_init_'
>> sander.o(.text+0x72): In function `MAIN__':
>> : undefined reference to `mpi_comm_rank_'
>> .....................
>> ......................
>> make[1]: *** [sander] Error 1
>> make[1]: Leaving directory `/home/liu/amber7/src/sander'
>> make: *** [install] Error 2
>> ===========
>>
>> Any help would be very appreciated!
>>
>> Regards!
>>
>> Liu
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
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adi2recv.o:
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U ch_debug_buf
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U ch_debug_buf
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chdebug.o:
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chchkdev.o:
U ch_debug_buf
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chshort.o:
U ch_debug_buf
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chflow.o:
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chinit.o:
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chnodename.o:
U gethostbyname
00000000 T MPID_Node_name
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chhetero.o:
U ch_debug_buf
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chtick.o:
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p4priv.o:
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queue.o:
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chcancel.o:
U ch_debug_buf
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ch_ldebug.o:
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isend.o:
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irecv.o:
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cancel.o:
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probe.o:
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start.o:
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testany.o:
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waitall.o:
U MPID_RecvComplete
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00000000 T PMPI_Waitall
send.o:
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00000000 T PMPI_Send
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eof_offset.o:
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U ADIOI_Free_fn
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U ADIOI_Malloc_fn
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U PMPI_Type_extent
U PMPI_Type_size
ad_write_coll.o:
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U ADIOI_Calc_file_domains
U ADIOI_Calc_my_off_len
U ADIOI_Calc_my_req
U ADIOI_Calc_others_req
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U ADIOI_Complete_async
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U MPIR_Err_setmsg
U MPIR_Status_set_bytes
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U PMPI_Alltoall
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U PMPI_Comm_size
U PMPI_Info_get
U PMPI_Irecv
U PMPI_Isend
U PMPI_Testall
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U PMPI_Type_free
U PMPI_Type_hindexed
U PMPI_Type_size
U stderr
U __strtol_internal
lock.o:
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U __errno_location
U fcntl
U fwrite
U PMPI_Abort
U stderr
ad_read_str.o:
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U ADIOI_Delete_flattened
U ADIOI_Flatlist
U ADIOI_Flatten_datatype
U ADIOI_Free_fn
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U ADIOI_GEN_ReadStrided_naive
U ADIOI_Malloc_fn
U ADIOI_Set_lock
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U memcpy
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U MPIR_Status_set_bytes
U PMPI_Info_get
U PMPI_Type_extent
U PMPI_Type_size
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ad_write_str.o:
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U ADIOI_Free_fn
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U fwrite
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U MPIR_Status_set_bytes
U PMPI_Abort
U PMPI_Info_get
U PMPI_Type_extent
U PMPI_Type_size
U stderr
U __strtol_internal
iscontig.o:
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U MPIR_Datatype_iscontig
get_fp_posn.o:
U ADIOI_Datatype_iscontig
U ADIOI_Flatlist
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U __divdi3
U PMPI_Type_extent
U PMPI_Type_size
ad_seek.o:
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U ADIOI_Error
U ADIOI_Flatlist
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U __divdi3
U __errno_location
U lseek
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U MPIR_Err_setmsg
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U PMPI_Type_extent
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ad_delete.o:
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U MPIR_Err_setmsg
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U strerror
U unlink
ad_flush.o:
U ADIOI_Error
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U __errno_location
U fsync
U MPIR_Err_setmsg
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U strerror
ad_hints.o:
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U ADIOI_Malloc_fn
U fwrite
U PMPI_Abort
U PMPI_Bcast
U PMPI_Comm_size
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U PMPI_Info_delete
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U strcpy
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error.o:
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U PMPI_Comm_rank
U PMPI_Error_string
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ad_fstype.o:
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U __errno_location
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U __lxstat
U MPIR_Err_setmsg
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U PMPI_Allreduce
U readlink
U statfs
U strchr
U __strdup
U strrchr
ad_get_sh_fp.o:
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U ADIOI_NFS_Get_shared_fp
U ADIOI_Set_lock
U ADIO_Open
U PMPI_Comm_dup
ad_set_sh_fp.o:
U ADIOI_NFS_Set_shared_fp
U ADIOI_Set_lock
U ADIO_Open
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U PMPI_Comm_dup
shfp_fname.o:
U ADIOI_Malloc_fn
00000000 T ADIOI_Shfp_fname
U PMPI_Bcast
U PMPI_Wtime
U sprintf
U strcat
U strcpy
U strrchr
byte_offset.o:
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U ADIOI_Flatlist
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U PMPI_Type_extent
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status_setb.o:
U MPID_Status_set_bytes
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ad_aggregate.o:
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U PMPI_Isend
U PMPI_Waitall
cb_config_list.o:
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ad_read_str_naive.o:
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U ADIOI_Set_lock
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U MPIR_Status_set_bytes
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gencheck.o:
U ADIOI_GEN_ReadStridedColl
U ADIOI_GEN_WriteStridedColl
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ad_set_view.o:
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U ADIOI_Delete_flattened
U ADIOI_Flatlist
U ADIOI_Flatten_datatype
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U PMPI_Type_commit
U PMPI_Type_contiguous
U PMPI_Type_free
U PMPI_Type_get_envelope
U PMPI_Type_size
ad_ufs_close.o:
U ADIOI_Error
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U close
U __errno_location
U MPIR_Err_setmsg
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U strerror
ad_ufs_read.o:
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U ADIOI_GEN_ReadStrided
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U lseek
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U PMPI_Type_size
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ad_ufs_open.o:
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U lseek
U MPIR_Err_setmsg
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U umask
ad_ufs_write.o:
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U ADIOI_GEN_WriteStrided
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U __errno_location
U lseek
U MPIR_Err_setmsg
U MPIR_Status_set_bytes
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U PMPI_Type_size
U strerror
U write
ad_ufs_done.o:
U ADIOI_Free_request
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U MPIR_Status_set_bytes
ad_ufs_fcntl.o:
U ADIOI_Datatype_iscontig
U ADIOI_Delete_flattened
U ADIOI_Error
U ADIOI_Flatlist
U ADIOI_Flatten_datatype
U ADIOI_Free_fn
U ADIOI_Malloc_fn
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U fwrite
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U MPIR_Err_setmsg
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U PMPI_Abort
U PMPI_Barrier
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U PMPI_Type_free
U PMPI_Type_get_envelope
U PMPI_Type_size
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U strerror
ad_ufs_iread.o:
U ADIOI_Malloc_request
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U ADIOI_UFS_ReadContig
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ad_ufs_iwrite.o:
U ADIOI_Malloc_request
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U PMPI_Get_elements
U PMPI_Type_size
ad_ufs_wait.o:
U ADIOI_Free_request
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U MPIR_Status_set_bytes
ad_ufs_resize.o:
U ADIOI_Error
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U __errno_location
U ftruncate
U MPIR_Err_setmsg
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U strerror
ad_ufs.o:
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U ADIOI_GEN_ReadStrided
U ADIOI_GEN_ReadStridedColl
U ADIOI_GEN_SeekIndividual
U ADIOI_GEN_SetInfo
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U ADIOI_UFS_Fcntl
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U ADIOI_UFS_IwriteContig
U ADIOI_UFS_IwriteStrided
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U ADIOI_UFS_ReadComplete
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U ADIOI_UFS_ReadDone
U ADIOI_UFS_Resize
U ADIOI_UFS_WriteComplete
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U ADIOI_UFS_WriteDone
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ad_nfs_close.o:
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U close
U __errno_location
U MPIR_Err_setmsg
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U strerror
ad_nfs_read.o:
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U ADIOI_Flatlist
U ADIOI_Flatten_datatype
U ADIOI_Free_fn
U ADIOI_Malloc_fn
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U MPIR_Status_set_bytes
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U PMPI_Type_size
U read
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ad_nfs_open.o:
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U __errno_location
U lseek
U MPIR_Err_setmsg
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U open
U strerror
U umask
ad_nfs_write.o:
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U ADIOI_Delete_flattened
U ADIOI_Error
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U ADIOI_Flatten_datatype
U ADIOI_Free_fn
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U strerror
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U write
ad_nfs_done.o:
U ADIOI_Free_request
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U MPIR_Status_set_bytes
ad_nfs_fcntl.o:
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U ADIOI_Error
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U ADIOI_Free_fn
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U strerror
ad_nfs_iread.o:
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ad_nfs_iwrite.o:
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ad_nfs_wait.o:
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U MPIR_Status_set_bytes
ad_nfs_resize.o:
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U MPIR_Err_setmsg
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U strerror
ad_nfs_setsh.o:
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U ADIOI_Set_lock
U ADIO_Open
U __errno_location
U lseek
U MPIR_Err_setmsg
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U PMPI_Comm_dup
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U write
ad_nfs_getsh.o:
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U ADIOI_Set_lock
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U lseek
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ad_nfs.o:
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U ADIOI_GEN_SetInfo
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closef.o:
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readf.o:
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openf.o:
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U ADIOI_Malloc_fn
U fwrite
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U PMPI_Abort
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writef.o:
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get_extentf.o:
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ireadf.o:
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iwritef.o:
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iotestf.o:
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iowaitf.o:
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seekf.o:
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deletef.o:
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U ADIOI_Malloc_fn
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U PMPI_Abort
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read_allf.o:
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read_atf.o:
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read_atallf.o:
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iread_atf.o:
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iwrite_atf.o:
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get_posnf.o:
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write_allf.o:
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write_atf.o:
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write_atallf.o:
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get_bytofff.o:
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set_viewf.o:
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U PMPI_Abort
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get_viewf.o:
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get_groupf.o:
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get_amodef.o:
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fsyncf.o:
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get_atomf.o:
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set_atomf.o:
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set_infof.o:
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get_infof.o:
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set_sizef.o:
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get_sizef.o:
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preallocf.o:
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rd_atallbf.o:
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rd_atallef.o:
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read_allbf.o:
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read_allef.o:
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wr_atallbf.o:
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wr_atallef.o:
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write_allbf.o:
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write_allef.o:
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get_posn_shf.o:
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iread_shf.o:
U MPI_File_iread_shared
U MPIO_Request_c2f
U PMPI_File_f2c
00000000 T pmpi_file_iread_shared__
read_shf.o:
U MPI_File_read_shared
U PMPI_File_f2c
00000000 T pmpi_file_read_shared__
write_shf.o:
U MPI_File_write_shared
U PMPI_File_f2c
00000000 T pmpi_file_write_shared__
iwrite_shf.o:
U MPI_File_iwrite_shared
U MPIO_Request_c2f
U PMPI_File_f2c
00000000 T pmpi_file_iwrite_shared__
seek_shf.o:
U MPI_File_seek_shared
U PMPI_File_f2c
00000000 T pmpi_file_seek_shared__
read_ordf.o:
U MPI_File_read_ordered
U PMPI_File_f2c
00000000 T pmpi_file_read_ordered__
read_ordef.o:
U MPI_File_read_ordered_end
U PMPI_File_f2c
00000000 T pmpi_file_read_ordered_end__
write_ordbf.o:
U MPI_File_write_ordered_begin
U PMPI_File_f2c
00000000 T pmpi_file_write_ordered_begin__
read_ordbf.o:
U MPI_File_read_ordered_begin
U PMPI_File_f2c
00000000 T pmpi_file_read_ordered_begin__
write_ordf.o:
U MPI_File_write_ordered
U PMPI_File_f2c
00000000 T pmpi_file_write_ordered__
write_ordef.o:
U MPI_File_write_ordered_end
U PMPI_File_f2c
00000000 T pmpi_file_write_ordered_end__
set_errhf.o:
U MPI_File_set_errhandler
U PMPI_File_f2c
00000000 T pmpi_file_set_errhandler__
get_errhf.o:
U MPI_File_get_errhandler
U PMPI_File_f2c
00000000 T pmpi_file_get_errhandler__
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Received on Mon May 03 2004 - 01:53:00 PDT
