Dear Darshan colleagues,
I recently installed darshan 3.1.5 on Shaheen, Cray XC40, we recently upgraded the OS to CLE6.up05 and using the 17.12 PrgEnv.
Compiling Scalapack with Cray Libsci fails with the error shown below with all programming environment. Similar issue was observed for other codes, like a simple petsc code.
After digging, it seems that it is related to darshan3.1.5 version recently installed on Shaheen. When unloading darshan, the compilation works fine with no issue.
The error is not appearing when using darshan 3.1.4.
ftn -o exe test_scalapack.f90
/opt/cray/dmapp/default/lib64/libdmapp.a(dmapp_internal.o): In function `_dmappi_is_pure_dmapp_job':
/home/abuild/rpmbuild/BUILD/cray-dmapp-7.1.1/src/dmapp_internal.c:1401: undefined reference to `__wrap_MPI_Init'
/opt/cray/pe/libsci/17.12.1/CRAY/8.6/x86_64/lib/libsci_cray_mpi_mp.a(blacs_exit_.o): In function `blacs_exit_':
/b/worker/csml-libsci-sles/build/mp/scalapack/BLACS/SRC/blacs_exit_.c:42: undefined reference to `__wrap_MPI_Finalize'
/opt/cray/pe/libsci/17.12.1/CRAY/8.6/x86_64/lib/libsci_cray_mpi_mp.a(blacs_pinfo_.o): In function `blacs_pinfo_':
/b/worker/csml-libsci-sles/build/mp/scalapack/BLACS/SRC/blacs_pinfo_.c:18: undefined reference to `__wrap_MPI_Init'
/opt/cray/pe/libsci/17.12.1/CRAY/8.6/x86_64/lib/libsci_cray_mpi_mp.a(blacs_pinfo_.oo): In function `Cblacs_pinfo':
/b/worker/csml-libsci-sles/build/mp/scalapack/BLACS/SRC/blacs_pinfo_.c:18: undefined reference to `__wrap_MPI_Init'
/opt/cray/pe/cce/8.6.5/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld: link errors found, deleting executable `exe'
/usr/bin/sha1sum: exe: No such file or directory
hadrib@cdl1:~> ll /usr/bin/sha1
sha1pass sha1sum
hadrib@cdl1:~> ll /usr/bin/sha1sum
-rwxr-xr-x 1 root root 43912 Aug 6 2016 /usr/bin/sha1sum
hadrib@cdl1:~> which sha1sum
/usr/bin/sha1sum
hadrib@cdl1:~> module list
Currently Loaded Modulefiles:
1) modules/3.2.10.6 9) pmi/5.0.13 17) atp/2.1.1
2) eproxy/2.0.22-6.0.5.0_2.1__g1ebe45c.ari 10) dmapp/7.1.1-6.0.5.0_49.8__g1125556.ari 18) perftools-base/7.0.0
3) cce/8.6.5 11) gni-headers/5.0.12-6.0.5.0_2.15__g2ef1ebc.ari 19) PrgEnv-cray/6.0.4
4) craype-network-aries 12) xpmem/2.2.4-6.0.5.0_4.8__g35d5e73.ari 20) cray-mpich/7.7.0
5) craype/2.5.13 13) job/2.2.2-6.0.5.0_8.47__g3c644b5.ari 21) slurm/slurm
6) cray-libsci/17.12.1 14) dvs/2.7_2.2.52-6.0.5.2_17.6__g5170dea 22) craype-haswell
7) udreg/2.3.2-6.0.5.0_13.12__ga14955a.ari 15) alps/6.5.28-6.0.5.0_18.6__g13a91b6.ari 23) texlive/2017
8) ugni/6.0.14-6.0.5.0_16.9__g19583bb.ari 16) rca/2.2.16-6.0.5.0_15.34__g5e09e6d.ari 24) darshan/3.1.5
hadrib@cdl1:~> module swap PrgEnv-cray/6.0.4 PrgEnv-intel
hadrib@cdl1:~> ftn -o exe_i test_scalapack.f90
/opt/cray/pe/libsci/17.12.1/INTEL/16.0/x86_64/lib/libsci_intel_mpi.a(blacs_exit_.o): In function `blacs_exit_':
blacs_exit_.c:(.text+0xe9): undefined reference to `__wrap_MPI_Finalize'
/opt/cray/pe/libsci/17.12.1/INTEL/16.0/x86_64/lib/libsci_intel_mpi.a(blacs_pinfo_.o): In function `blacs_pinfo_':
blacs_pinfo_.c:(.text+0x9b): undefined reference to `__wrap_MPI_Init'
/opt/cray/pe/libsci/17.12.1/INTEL/16.0/x86_64/lib/libsci_intel_mpi.a(blacs_pinfo_.oo): In function `Cblacs_pinfo':
blacs_pinfo_.c:(.text+0x9b): undefined reference to `__wrap_MPI_Init'
hadrib@cdl1:~>
hadrib@cdl1:~>
hadrib@cdl1:~> module swap PrgEnv-intel/6.0.4 PrgEnv-gnu
PrgEnv-gnu PrgEnv-gnu/6.0.4
hadrib@cdl1:~> module swap PrgEnv-intel/6.0.4 PrgEnv-gnu
hadrib@cdl1:~> ftn -o exe_i test_scalapack.f90
/opt/cray/pe/libsci/17.12.1/GNU/6.1/x86_64/lib/libsci_gnu_61_mpi.a(blacs_exit_.o): In function `blacs_exit_':
blacs_exit_.c:(.text+0xdb): undefined reference to `__wrap_MPI_Finalize'
/opt/cray/pe/libsci/17.12.1/GNU/6.1/x86_64/lib/libsci_gnu_61_mpi.a(blacs_pinfo_.o): In function `blacs_pinfo_':
blacs_pinfo_.c:(.text+0xb3): undefined reference to `__wrap_MPI_Init'
/opt/cray/pe/libsci/17.12.1/GNU/6.1/x86_64/lib/libsci_gnu_61_mpi.a(blacs_pinfo_.oo): In function `Cblacs_pinfo':
blacs_pinfo_.c:(.text+0xb3): undefined reference to `__wrap_MPI_Init'
=====
implicit none
integer :: n, nb ! problem size and block size
integer :: myunit ! local output unit number
integer :: myArows, myAcols ! size of local subset of global array
integer :: i,j, igrid,jgrid, iproc,jproc, myi,myj, p
real*8, dimension(:,:), allocatable :: myA,myB,myC
integer :: numroc ! blacs routine
integer :: me, procs, icontxt, prow, pcol, myrow, mycol ! blacs data
integer :: info ! scalapack return value
integer, dimension(9) :: ides_a, ides_b, ides_c ! scalapack array desc
open(unit=1,file="ABCp.dat",status="old",form="formatted")
read(1,*)prow
read(1,*)pcol
read(1,*)n
read(1,*)nb
close(1)
if (((n/nb) < prow) .or. ((n/nb) < pcol)) then
print *,"Problem size too small for processor set!"
stop 100
endif
call blacs_pinfo (me,procs)
call blacs_get (0, 0, icontxt)
call blacs_gridinit(icontxt, 'R', prow, pcol)
call blacs_gridinfo(icontxt, prow, pcol, myrow, mycol)
myunit = 10+me
write(myunit,*)"--------"
write(myunit,*)"Output for processor ",me," to unit ",myunit
write(myunit,*)"Proc ",me,": myrow, mycol in p-array is ", &
myrow, mycol
myArows = numroc(n, nb, myrow, 0, prow)
myAcols = numroc(n, nb, mycol, 0, pcol)
write(myunit,*)"Size of global array is ",n," x ",n
write(myunit,*)"Size of block is ",nb," x ",nb
write(myunit,*)"Size of local array is ",myArows," x ",myAcols
allocate(myA(myArows,myAcols))
allocate(myB(myArows,myAcols))
allocate(myC(myArows,myAcols))
do i=1,n
call g2l(i,n,prow,nb,iproc,myi)
if (myrow==iproc) then
do j=1,n
call g2l(j,n,pcol,nb,jproc,myj)
if (mycol==jproc) then
myA(myi,myj) = real(i+j)
myB(myi,myj) = real(i-j)
myC(myi,myj) = 0.d0
endif
enddo
endif
enddo
! Prepare array descriptors for ScaLAPACK
ides_a(1) = 1 ! descriptor type
ides_a(2) = icontxt ! blacs context
ides_a(3) = n ! global number of rows
ides_a(4) = n ! global number of columns
ides_a(5) = nb ! row block size
ides_a(6) = nb ! column block size
ides_a(7) = 0 ! initial process row
ides_a(8) = 0 ! initial process column
ides_a(9) = myArows ! leading dimension of local array
do i=1,9
ides_b(i) = ides_a(i)
ides_c(i) = ides_a(i)
enddo
! Call ScaLAPACK library routine
call pdgemm('T','T',n,n,n,1.0d0, myA,1,1,ides_a, &
myB,1,1,ides_b,0.d0, &
myC,1,1,ides_c )
! Print results
call g2l(n,n,prow,nb,iproc,myi)
call g2l(n,n,pcol,nb,jproc,myj)
if ((myrow==iproc) .and. (mycol==jproc)) &
write(*,*) 'c(',n,n,')=',myC(myi,myj)
! Deallocate the local arrays
deallocate(myA, myB, myC)
! End blacs for processors that are used
call blacs_gridexit(icontxt)
call blacs_exit(0)
end
! convert global index to local index in block-cyclic distribution
subroutine g2l(i,n,np,nb,p,il)
implicit none
integer :: i ! global array index, input
integer :: n ! global array dimension, input
integer :: np ! processor array dimension, input
integer :: nb ! block size, input
integer :: p ! processor array index, output
integer :: il ! local array index, output
integer :: im1
im1 = i-1
p = mod((im1/nb),np)
il = (im1/(np*nb))*nb + mod(im1,nb) + 1
return
end
! convert local index to global index in block-cyclic distribution
subroutine l2g(il,p,n,np,nb,i)
implicit none
integer :: il ! local array index, input
integer :: p ! processor array index, input
integer :: n ! global array dimension, input
integer :: np ! processor array dimension, input
integer :: nb ! block size, input
integer :: i ! global array index, output
integer :: ilm1
ilm1 = il-1
i = (((ilm1/nb) * np) + p)*nb + mod(ilm1,nb) + 1
return
end
-------
Bilel Hadri, PhD
Computational Scientist
KAUST Supercomputing Lab
Al Khawarizmi Bldg. (1) Office 126
4700 King Abdullah University of Science and Technology
Thuwal 23955-6900
Kingdom of Saudi Arabia
Office Phone: +966 12 808 0654
Cell Phone: + 966 544 700 893
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