I would not assume that parallel make works with Amber 11 + AmberTools 1.5.
Try make without the -j option. I've built Amber 11 + AmberTools 1.5 with
both Intel 12.1.0 compilers and GNU compilers (4.4.6, 4.5.3, and a couple
others), so I know it works.
HTH,
Jason
On Wed, Jan 4, 2012 at 11:17 AM, Lucas A. Defelipe <ldefelipe.gmail.com>wrote:
> Hello,
> I am trying to recompile AMBER11 with AmberTools 1.5 with the
> latest bugfixes using Intel Compilers version 12. I've also tried GNU
> compilers and getting the same error. I include the log pasted below.
> Thanks in advance.
>
> Kind Regards,
> Lic. Lucas A. Defelipe
> Laboratorio de Bioinformática Estructural - QB6
> Departamento de Química Biológica, FCEyN - UBA e INQUIMAE-CONICET
> 4to. piso Ciudad Universitaria Pabellón II
> Int. Guiraldes 2620 C1428EHA
> Ciudad Autónoma de Buenos Aires, Argentina
> Tel: +54 11 4576 3300 int 205
> http://bioinf.qb.fcen.uba.ar
>
> Output
> /bin/bash ../libtool --mode=link icc -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -DBINTRAJ -ip -O3 -axSTPW -DBINTRAJ -DHASGZ -o
> fftw_test fftw_test.o test_main.o ../fftw/libdfftw.la -lm
> mkdir .libs
> icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -ip -O3 -axSTPW
> -DBINTRAJ -DHASGZ -o fftw_test fftw_test.o test_main.o
> ../fftw/.libs/libdfftw.a -lm
> icc: command line remark #10279: option '-axS' is deprecated and will be
> removed in a future release. See '-help deprecated'
> icc: command line remark #10279: option '-axT' is deprecated and will be
> removed in a future release. See '-help deprecated'
> icc: command line remark #10279: option '-axP' is deprecated and will be
> removed in a future release. See '-help deprecated'
> icc: command line remark #10279: option '-axW' is deprecated and will be
> removed in a future release. See '-help deprecated'
> fftw_test.o: In function `test_speed_aux':
> fftw_test.c:(.text+0x3d2): undefined reference to `fftw'
> fftw_test.o: In function `fftw_plan_hook_function':
> fftw_test.c:(.text+0x17f7): undefined reference to `fftw'
> fftw_test.c:(.text+0x1822): undefined reference to `fftw'
> fftw_test.c:(.text+0x18d0): undefined reference to `fftw'
> fftw_test.c:(.text+0x18f8): undefined reference to `fftw'
> fftw_test.o:fftw_test.c:(.text+0x1f47): more undefined references to `fftw'
> follow
> fftw_test.o: In function `test_out_of_place':
> fftw_test.c:(.text+0xbc1d): undefined reference to `fftw_one'
> fftw_test.o: In function `test_in_place':
> fftw_test.c:(.text+0xbf09): undefined reference to `fftw'
> fftw_test.c:(.text+0xc039): undefined reference to `fftw'
> fftw_test.c:(.text+0xc13e): undefined reference to `fftw_one'
> fftw_test.o: In function `test_ergun':
> fftw_test.c:(.text+0xc413): undefined reference to `fftw'
> fftw_test.c:(.text+0xc43e): undefined reference to `fftw'
> fftw_test.c:(.text+0xc4ed): undefined reference to `fftw'
> fftw_test.c:(.text+0xc515): undefined reference to `fftw'
> fftw_test.c:(.text+0xcb54): undefined reference to `fftw'
> fftw_test.o:fftw_test.c:(.text+0xcb7c): more undefined references to `fftw'
> follow
> test_main.o: In function `handle_option':
> test_main.c:(.text+0x20c4): undefined reference to `fftw_version'
> ../fftw/.libs/libdfftw.a(planner.o): In function `planner_normal':
> planner.c:(.text+0x8c9): undefined reference to `fftw'
> planner.c:(.text+0xe48): undefined reference to `fftw'
> planner.c:(.text+0x143a): undefined reference to `fftw'
> planner.c:(.text+0x1670): undefined reference to `fftw'
> planner.c:(.text+0x19bd): undefined reference to `fftw'
> ../fftw/.libs/libdfftw.a(fftwnd.o):fftwnd.c:(.text+0x2189): more undefined
> references to `fftw' follow
> ../fftw/.libs/libdfftw.a(malloc.o): In function `fftw_check_memory_leaks':
> malloc.c:(.text+0xf5): undefined reference to `fftw_twiddle_size'
> malloc.c:(.text+0x120): undefined reference to `fftw_twiddle_size'
> ../fftw/.libs/libdfftw.a(putils.o): In function `fftw_make_node_twiddle':
> putils.c:(.text+0x164): undefined reference to `fftw_create_twiddle'
> ../fftw/.libs/libdfftw.a(putils.o): In function `fftw_make_node_hc2hc':
> putils.c:(.text+0x1f2): undefined reference to `fftw_create_twiddle'
> ../fftw/.libs/libdfftw.a(putils.o): In function `fftw_make_node_generic':
> putils.c:(.text+0x26e): undefined reference to `fftw_create_twiddle'
> ../fftw/.libs/libdfftw.a(putils.o): In function `fftw_make_node_rgeneric':
> putils.c:(.text+0x337): undefined reference to `fftw_create_twiddle'
> ../fftw/.libs/libdfftw.a(putils.o): In function `fftw_complete_twiddle':
> putils.c:(.text+0x48c): undefined reference to `fftw_create_twiddle'
> ../fftw/.libs/libdfftw.a(putils.o):putils.c:(.text+0x49e): more undefined
> references to `fftw_create_twiddle' follow
> ../fftw/.libs/libdfftw.a(putils.o): In function `destroy_tree':
> putils.c:(.text+0x607): undefined reference to `fftw_destroy_twiddle'
> putils.c:(.text+0x617): undefined reference to `fftw_destroy_twiddle'
> putils.c:(.text+0x627): undefined reference to `fftw_destroy_twiddle'
> putils.c:(.text+0x657): undefined reference to `fftw_destroy_twiddle'
> putils.c:(.text+0x667): undefined reference to `fftw_destroy_twiddle'
> ../fftw/.libs/libdfftw.a(rader.o): In function `fftw_twiddle_rader':
> rader.c:(.text+0x228): undefined reference to `fftw_executor_simple'
> rader.c:(.text+0x479): undefined reference to `fftw_executor_simple'
> ../fftw/.libs/libdfftw.a(rader.o): In function `fftwi_twiddle_rader':
> rader.c:(.text+0x778): undefined reference to `fftw_executor_simple'
> rader.c:(.text+0x9c9): undefined reference to `fftw_executor_simple'
> ../fftw/.libs/libdfftw.a(rader.o): In function `fftw_make_node_rader':
> rader.c:(.text+0xc14): undefined reference to `fftw_create_twiddle'
> rader.c:(.text+0xe9c): undefined reference to `fftw_executor_simple'
> make[3]: *** [fftw_test] Error 1
> make[3]: *** Waiting for unfinished jobs....
> make[3]: Leaving directory
> `/home/lucas/amber11_prueba/AmberTools/src/fftw-2.1.5/tests'
> make[2]: *** [install-recursive] Error 1
> make[2]: Leaving directory
> `/home/lucas/amber11_prueba/AmberTools/src/fftw-2.1.5'
> make[1]: *** [-ldfftw] Error 2
> make[1]: Leaving directory `/home/lucas/amber11_prueba/AmberTools/src/rism'
> make: *** [serial] Error 2
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jan 04 2012 - 12:00:03 PST
