Please Help: SuitSparse, UMF pack do not work!!!!!!! ;( ;(

Please Help: SuitSparse, UMF pack do not work!!!!!!! ;( ;(

Hi all.

Please, help me: I am experiencing a lot of huge problems in running my sims.   I have CENTOS 6, unfortunately, and Linux Free - Unsupported compilers, C++ and Fortran. 

I need the SuiteSparse and UMF Pack for some fluid-structure simulation problems. I cannot run my sims, the libs seem to be not found by the compiler. I have compiled and installed all the libraries and I use the following script to compile my C++ code:

#!/bin/sh

g++ -O3 -DMTL_HAS_BLAS -DMTL_HAS_UMFPACK main.cpp -fpermissive /opt/SuiteSparse/AMD/Lib/libamd.a /opt/SuiteSparse/COLAMD/Lib/libcolamd.a /opt/GotoBLAS2/libgoto2.a -lpthread /opt/SuiteSparse/UMFPACK/Lib/libumfpack.a -I/opt/SuiteSparse/AMD/Include -I/opt/SuiteSparse/UMFPACK/Include/ -I/opt/SuiteSparse/UFconfig -I/opt/mtl4 -o main

The answer is the following:

$ ./esegui.sh

/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_l_free.o): In function `umf_l_free':
umf_free.c:(.text+0xc): undefined reference to `amd_free'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_l_malloc.o): In function `umf_l_malloc':
umf_malloc.c:(.text+0x2b): undefined reference to `amd_malloc'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_l_realloc.o): In function `umf_l_realloc':
umf_realloc.c:(.text+0x33): undefined reference to `amd_realloc'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umfpack_gn_tictoc.o): In function `umfpack_toc':
umfpack_tictoc.c:(.text+0x5): undefined reference to `SuiteSparse_time'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umfpack_gn_tictoc.o): In function `umfpack_tic':
umfpack_tictoc.c:(.text+0x25): undefined reference to `SuiteSparse_time'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_dl_kernel_init.o): In function `umfdl_kernel_init':
umf_kernel_init.c:(.text+0xd67): undefined reference to `amd_l_valid'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_dl_local_search.o): In function `umfdl_local_search':
umf_local_search.c:(.text+0x140c): undefined reference to `dgemv_'
umf_local_search.c:(.text+0x148c): undefined reference to `dtrsv_'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umfpack_dl_qsymbolic.o): In function `symbolic_analysis':
umfpack_qsymbolic.c:(.text+0x29f): undefined reference to `amd_l_defaults'
umfpack_qsymbolic.c:(.text+0x137d): undefined reference to `amd_l_aat'
umfpack_qsymbolic.c:(.text+0x384d): undefined reference to `amd_l_defaults'
umfpack_qsymbolic.c:(.text+0x4ae5): undefined reference to `amd_l2'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_l_analyze.o): In function `umf_l_analyze':
umf_analyze.c:(.text+0x802): undefined reference to `amd_l_postorder'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_l_colamd.o): In function `umf_l_colamd':
umf_colamd.c:(.text+0x16ea): undefined reference to `amd_l_postorder'
umf_colamd.c:(.text+0x19f6): undefined reference to `amd_l_postorder'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_l_cholmod.o): In function `umf_l_cholmod':
umf_cholmod.c:(.text+0xad): undefined reference to `cholmod_l_start'
umf_cholmod.c:(.text+0x10e): undefined reference to `amd_malloc'
umf_cholmod.c:(.text+0x13e): undefined reference to `amd_realloc'
umf_cholmod.c:(.text+0x150): undefined reference to `amd_calloc'
umf_cholmod.c:(.text+0x162): undefined reference to `amd_free'
umf_cholmod.c:(.text+0x206): undefined reference to `cholmod_l_analyze'
umf_cholmod.c:(.text+0x21e): undefined reference to `cholmod_l_free_sparse'
umf_cholmod.c:(.text+0x2cc): undefined reference to `cholmod_l_free_factor'
umf_cholmod.c:(.text+0x2e3): undefined reference to `cholmod_l_print_common'
umf_cholmod.c:(.text+0x2eb): undefined reference to `cholmod_l_finish'
umf_cholmod.c:(.text+0x489): undefined reference to `cholmod_l_transpose'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_dl_blas3_update.o): In function `umfdl_blas3_update':
umf_blas3_update.c:(.text+0x6d9): undefined reference to `dtrsm_'
umf_blas3_update.c:(.text+0x8e3): undefined reference to `dger_'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_dl_transpose.o): In function `umfdl_transpose':
umf_transpose.c:(.text+0x52f): undefined reference to `amd_l_valid'
collect2: ld returned 1 exit status

Please, note that all the things the compiler does not find ARE in the directories I point to in the script......

Do I make any mistake in the compilation script?

Please help me......!!!!!!!!!!!! :( :(

 

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Para obtener más información sobre las optimizaciones del compilador, consulte el aviso sobre la optimización.
Imagen de Georg Zitzlsberger (Intel)

Hello,

add /opt/SuiteSparse/AMD/Lib/libamd.a once more at the end:

g++ -O3 -DMTL_HAS_BLAS -DMTL_HAS_UMFPACK main.cpp -fpermissive /opt/SuiteSparse/AMD/Lib/libamd.a /opt/SuiteSparse/COLAMD/Lib/libcolamd.a /opt/GotoBLAS2/libgoto2.a -lpthread /opt/SuiteSparse/UMFPACK/Lib/libumfpack.a -I/opt/SuiteSparse/AMD/Include -I/opt/SuiteSparse/UMFPACK/Include/ -I/opt/SuiteSparse/UFconfig -I/opt/mtl4 -o main /opt/SuiteSparse/AMD/Lib/libamd.a

I'm going to close the other threads from you as they seem to be duplicates.

Best regards,

Georg Zitzlsberger

Hello!!!

thanks truly much for Your help And sorry for the double post...

unfortunately, it doesn't work, but it's got better:

]$ ./esegui.sh
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umfpack_gn_tictoc.o): In function `umfpack_toc':
umfpack_tictoc.c:(.text+0x5): undefined reference to `SuiteSparse_time'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umfpack_gn_tictoc.o): In function `umfpack_tic':
umfpack_tictoc.c:(.text+0x25): undefined reference to `SuiteSparse_time'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_dl_local_search.o): In function `umfdl_local_search':
umf_local_search.c:(.text+0x140c): undefined reference to `dgemv_'
umf_local_search.c:(.text+0x148c): undefined reference to `dtrsv_'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_l_cholmod.o): In function `umf_l_cholmod':
umf_cholmod.c:(.text+0xad): undefined reference to `cholmod_l_start'
umf_cholmod.c:(.text+0x206): undefined reference to `cholmod_l_analyze'
umf_cholmod.c:(.text+0x21e): undefined reference to `cholmod_l_free_sparse'
umf_cholmod.c:(.text+0x2cc): undefined reference to `cholmod_l_free_factor'
umf_cholmod.c:(.text+0x2e3): undefined reference to `cholmod_l_print_common'
umf_cholmod.c:(.text+0x2eb): undefined reference to `cholmod_l_finish'
umf_cholmod.c:(.text+0x489): undefined reference to `cholmod_l_transpose'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_dl_blas3_update.o): In function `umfdl_blas3_update':
umf_blas3_update.c:(.text+0x6d9): undefined reference to `dtrsm_'
umf_blas3_update.c:(.text+0x8e3): undefined reference to `dger_'
collect2: ld returned 1 exit status
ESECUZIONE beta 5, batra
[tesisti@Grande-Mazinga batra_def]$ nohup: appending output to `nohup.out'
nohup: failed to run command `./main_batra': No such file or directory

thanks and the best reregards 

herger

Imagen de Georg Zitzlsberger (Intel)

Hello,

also add /opt/SuiteSparse/COLAMD/Lib/libcolamd.a and/or /opt/GotoBLAS2/libgoto2.a at the end as well.

The GNU* linker is single pass and symbol references to static libraries found will be only resolved with subsequently specifying those libraries.

Best regards,

Georg Zitzlsberger

Hello!

Thanks again truly much for Your help.

I have re-linked both the librearies (I tried all the possibile permutations, aand I think that both were needed to be re-linked).     Now the error message is:

./esegui.sh
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umfpack_gn_tictoc.o): In function `umfpack_toc':
umfpack_tictoc.c:(.text+0x5): undefined reference to `SuiteSparse_time'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umfpack_gn_tictoc.o): In function `umfpack_tic':
umfpack_tictoc.c:(.text+0x25): undefined reference to `SuiteSparse_time'
/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a(umf_l_cholmod.o): In function `umf_l_cholmod':
umf_cholmod.c:(.text+0xad): undefined reference to `cholmod_l_start'
umf_cholmod.c:(.text+0x206): undefined reference to `cholmod_l_analyze'
umf_cholmod.c:(.text+0x21e): undefined reference to `cholmod_l_free_sparse'
umf_cholmod.c:(.text+0x2cc): undefined reference to `cholmod_l_free_factor'
umf_cholmod.c:(.text+0x2e3): undefined reference to `cholmod_l_print_common'
umf_cholmod.c:(.text+0x2eb): undefined reference to `cholmod_l_finish'
umf_cholmod.c:(.text+0x489): undefined reference to `cholmod_l_transpose'
collect2: ld returned 1 exit status
ESECUZIONE beta 5, batra
[tesisti@Grande-Mazinga batra_def]$ nohup: appending output to `nohup.out'
nohup: failed to run command `./main_batra': No such file or directory

I tried to add at the end of the script 

/opt/SuiteSparse/UMFPACK/Lib/libumfpack.a

or 

-lpthread /opt/SuiteSparse/UMFPACK/Lib/libumfpack.a

but with no results...

Thanks again for Your time and Your pacience, best regards

Herger

For the sake of completeness, I attach here the actual script to compile:

#!/bin/sh

g++ -O3 -DMTL_HAS_BLAS -DMTL_HAS_UMFPACK main.cpp -fpermissive /opt/SuiteSparse/AMD/Lib/libamd.a /opt/SuiteSparse/COLAMD/Lib/libcolamd.a /opt/GotoBLAS2/libgoto2.a -lpthread /opt/SuiteSparse/UMFPACK/Lib/libumfpack.a -I/opt/SuiteSparse/AMD/Include -I/opt/SuiteSparse/UMFPACK/Include/ -I/opt/SuiteSparse/UFconfig -I/opt/mtl4 -o main_batra /opt/SuiteSparse/AMD/Lib/libamd.a /opt/SuiteSparse/COLAMD/Lib/libcolamd.a /opt/GotoBLAS2/libgoto2.a

echo "ESECUZIONE beta 5, batra"

nohup ./main_batra &

Thanks again and the best regards

H

>>>>...the SuiteSparse and UMF Pack...
>>...
>>but with no results...

Hi,

Unfortunately, your linker problems are not related to Intel C++ compiler. Even if Georg gave you really good recommendations you need to ask for help on a forum(s) dedicated to SuiteSparse and UMF Pack software.

Best regards,
Sergey

Sorry... 

Thanks truly much to both of You, best regards

H

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