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Subject: Re: [OMPI devel] Error compiling
From: R C (recifx_at_[hidden])
Date: 2012-12-23 16:43:05


I put /usr/local/lib at the beginning of LD_LIBRARY_PATH and I get:
$ ompi_info
[RCAsus1:20105] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_errmgr_default:
/usr/local/lib/openmpi/mca_errmgr_default.so: undefined symbol:
orte_errmgr_base_output (ignored)
[RCAsus1:20105] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_ess_slurmd:
/usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol:
orte_nid_t_class (ignored)
[RCAsus1:20105] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_grpcomm_basic:
/usr/local/lib/openmpi/mca_grpcomm_basic.so: undefined symbol:
opal_profile_file (ignored)
[RCAsus1:20105] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_routed_cm:
/usr/local/lib/openmpi/mca_routed_cm.so: undefined symbol:
orte_message_event_t_class (ignored)
[RCAsus1:20105] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_routed_linear:
/usr/local/lib/openmpi/mca_routed_linear.so: undefined symbol:
orte_message_event_t_class (ignored)
                 Package: Open MPI rc_at_RCAsus1 Distribution
                Open MPI: 1.9a1r27719
  Open MPI repo revision: r27719
   Open MPI release date: Unreleased developer copy
                Open RTE: 1.9a1r27719

and now when I try:

$ mpicc -o hw hello.c

it seems to compile, but from:
$mpirun -np 4 hw
RCAsus1:26668] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_ess_slurmd:
/usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol:
orte_nid_t_class (ignored)
[RCAsus1:26668] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_errmgr_default:
/usr/local/lib/openmpi/mca_errmgr_default.so: undefined symbol:
orte_errmgr_base_output (ignored)
[RCAsus1:26668] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_routed_cm:
/usr/local/lib/openmpi/mca_routed_cm.so: undefined symbol:
orte_message_event_t_class (ignored)
[RCAsus1:26668] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_routed_linear:
/usr/local/lib/openmpi/mca_routed_linear.so: undefined symbol:
orte_message_event_t_class (ignored)
[RCAsus1:26668] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_grpcomm_basic:
/usr/local/lib/openmpi/mca_grpcomm_basic.so: undefined symbol:
opal_profile_file (ignored)
[RCAsus1:26668] *** Process received signal ***
[RCAsus1:26668] Signal: Segmentation fault (11)
[RCAsus1:26668] Signal code: (128)
[RCAsus1:26668] Failing at address: (nil)
[RCAsus1:26668] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0)
[0x7f0e31d54cb0]
[RCAsus1:26668] [ 1]
/usr/local/lib/openmpi/mca_rmaps_load_balance.so(+0xca8) [0x7f0e2f720ca8]
[RCAsus1:26668] [ 2]
/usr/local/lib/libopen-rte.so.0(orte_rmaps_base_map_job+0x1ba)
[0x7f0e3226b09a]
[RCAsus1:26668] [ 3]
/usr/local/lib/libopen-pal.so.0(opal_libevent2019_event_base_loop+0x626)
[0x7f0e31fb97e6]
[RCAsus1:26668] [ 4] /usr/local/lib/libopen-pal.so.0(opal_progress+0xb3)
[0x7f0e31f87483]
[RCAsus1:26668] [ 5] mpirun(orterun+0x10fb) [0x404b8d]
[RCAsus1:26668] [ 6] mpirun(main+0x20) [0x4036ec]
[RCAsus1:26668] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f0e319a776d]
[RCAsus1:26668] [ 8] mpirun() [0x4035e9]
[RCAsus1:26668] *** End of error message ***
Segmentation fault (core dumped)

504:5 $ mpicc -o hw hello.c
[04:37 PM][rc_at_RCAsus1] [~/Dropbox/tst]
505:6 $ mpirun -np 4 hw
[RCAsus1:26668] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_ess_slurmd:
/usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol:
orte_nid_t_class (ignored)
[RCAsus1:26668] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_errmgr_default:
/usr/local/lib/openmpi/mca_errmgr_default.so: undefined symbol:
orte_errmgr_base_output (ignored)
[RCAsus1:26668] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_routed_cm:
/usr/local/lib/openmpi/mca_routed_cm.so: undefined symbol:
orte_message_event_t_class (ignored)
[RCAsus1:26668] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_routed_linear:
/usr/local/lib/openmpi/mca_routed_linear.so: undefined symbol:
orte_message_event_t_class (ignored)
[RCAsus1:26668] mca: base: component_find: unable to open
/usr/local/lib/openmpi/mca_grpcomm_basic:
/usr/local/lib/openmpi/mca_grpcomm_basic.so: undefined symbol:
opal_profile_file (ignored)
[RCAsus1:26668] *** Process received signal ***
[RCAsus1:26668] Signal: Segmentation fault (11)
[RCAsus1:26668] Signal code: (128)
[RCAsus1:26668] Failing at address: (nil)
[RCAsus1:26668] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0)
[0x7f0e31d54cb0]
[RCAsus1:26668] [ 1]
/usr/local/lib/openmpi/mca_rmaps_load_balance.so(+0xca8) [0x7f0e2f720ca8]
[RCAsus1:26668] [ 2]
/usr/local/lib/libopen-rte.so.0(orte_rmaps_base_map_job+0x1ba)
[0x7f0e3226b09a]
[RCAsus1:26668] [ 3]
/usr/local/lib/libopen-pal.so.0(opal_libevent2019_event_base_loop+0x626)
[0x7f0e31fb97e6]
[RCAsus1:26668] [ 4] /usr/local/lib/libopen-pal.so.0(opal_progress+0xb3)
[0x7f0e31f87483]
[RCAsus1:26668] [ 5] mpirun(orterun+0x10fb) [0x404b8d]
[RCAsus1:26668] [ 6] mpirun(main+0x20) [0x4036ec]
[RCAsus1:26668] [ 7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f0e319a776d]
[RCAsus1:26668] [ 8] mpirun() [0x4035e9]
[RCAsus1:26668] *** End of error message ***
Segmentation fault (core dumped)

Thanks for your assistance.

On Sun, Dec 23, 2012 at 4:08 PM, Ralph Castain <rhc_at_[hidden]> wrote:

> Do you have your LD_LIBRARY_PATH set correctly? You want your prefix
> location to be at the front so you don't pickup something from the default
> system installation.
>
> On Dec 23, 2012, at 12:39 PM, R C <recifx_at_[hidden]> wrote:
>
> Thanks, r27719 compiles but I get an error when I try:
> $/usr/local/bin/ompi_info
> /usr/local/bin/ompi_info: symbol lookup error: /usr/local/bin/ompi_info:
> undefined symbol: mca_fbtl_base_components_opened
>
> and when I tried to compile a test program:
> $ mpicc -o hw hello.c
> mpicc: Symbol `opal_show_help' has different size in shared object,
> consider re-linking
>
>
>
> On Sun, Dec 23, 2012 at 2:55 PM, Ralph Castain <rhc_at_[hidden]> wrote:
>
>> Sigh - sorry about that. Guess we'll have to feel our way down the
>> various tools. I've committed a fix that -should- resolve this for the rest
>> of the tools in the OMPI layer. Please let me know how it works for you.
>>
>> Ralph
>>
>> On Dec 23, 2012, at 10:56 AM, R C <recifx_at_[hidden]> wrote:
>>
>>
>> Thanks again for looking into this.
>> With r27717, 'make all' gives me the error:
>>
>> Making all in tools/ompi_info
>> make[2]: Entering directory
>> `/home/rc/Downloads/ompi/objd/ompi/tools/ompi_info'
>> CC ompi_info.o
>> CC param.o
>> ../../../../ompi/tools/ompi_info/param.c: In function
>> ‘ompi_info_do_config’:
>> ../../../../ompi/tools/ompi_info/param.c:238:17: warning: ignoring return
>> value of ‘asprintf’, declared with attribute warn_unused_result
>> [-Wunused-result]
>> ../../../../ompi/tools/ompi_info/param.c:252:17: warning: ignoring return
>> value of ‘asprintf’, declared with attribute warn_unused_result
>> [-Wunused-result]
>> ../../../../ompi/tools/ompi_info/param.c:259:17: warning: ignoring return
>> value of ‘asprintf’, declared with attribute warn_unused_result
>> [-Wunused-result]
>> ../../../../ompi/tools/ompi_info/param.c:271:13: warning: ignoring return
>> value of ‘asprintf’, declared with attribute warn_unused_result
>> [-Wunused-result]
>> ../../../../ompi/tools/ompi_info/param.c:274:13: warning: ignoring return
>> value of ‘asprintf’, declared with attribute warn_unused_result
>> [-Wunused-result]
>> CC components.o
>> ../../../../ompi/tools/ompi_info/components.c: In function
>> ‘ompi_info_register_components’:
>> ../../../../ompi/tools/ompi_info/components.c:106:17: warning: ignoring
>> return value of ‘asprintf’, declared with attribute warn_unused_result
>> [-Wunused-result]
>> ../../../../ompi/tools/ompi_info/components.c:109:21: warning: ignoring
>> return value of ‘asprintf’, declared with attribute warn_unused_result
>> [-Wunused-result]
>> ../../../../ompi/tools/ompi_info/components.c:113:21: warning: ignoring
>> return value of ‘asprintf’, declared with attribute warn_unused_result
>> [-Wunused-result]
>> CC version.o
>> ../../../../ompi/tools/ompi_info/version.c: In function
>> ‘ompi_info_show_ompi_version’:
>> ../../../../ompi/tools/ompi_info/version.c:125:13: warning: ignoring
>> return value of ‘asprintf’, declared with attribute warn_unused_result
>> [-Wunused-result]
>> ../../../../ompi/tools/ompi_info/version.c:134:13: warning: ignoring
>> return value of ‘asprintf’, declared with attribute warn_unused_result
>> [-Wunused-result]
>> ../../../../ompi/tools/ompi_info/version.c:137:13: warning: ignoring
>> return value of ‘asprintf’, declared with attribute warn_unused_result
>> [-Wunused-result]
>> CCLD ompi_info
>> /usr/bin/ld: version.o: undefined reference to symbol
>> 'orte_info_type_orte'
>> /usr/bin/ld: note: 'orte_info_type_orte' is defined in DSO
>> /home/rc/Downloads/ompi/objd/orte/.libs/libopen-rte.so.0 so try adding it
>> to the linker command line
>> /home/rc/Downloads/ompi/objd/orte/.libs/libopen-rte.so.0: could not read
>> symbols: Invalid operation
>> collect2: error: ld returned 1 exit status
>> make[2]: *** [ompi_info] Error 1
>> make[2]: Leaving directory
>> `/home/rc/Downloads/ompi/objd/ompi/tools/ompi_info'
>> make[1]: *** [all-recursive] Error 1
>> make[1]: Leaving directory `/home/rc/Downloads/ompi/objd/ompi'
>> make: *** [all-recursive] Error 1
>>
>>