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ERROR:/usr/bin/ar: two different operation options specified

MabelSue

MabelSue
New Member
Hello, could somebody help me?

It happened when I tryed to port Cesm(./case.build)(mct).

Searching results showed GUN ar specified dynamic libs(.o) before statistic libs(.a)

But I don't know how to do.
_______________________________________

Calling /my_cesm_sandbox/cime/src/build_scripts/buildlib.mct
ERROR: /my_cesm_sandbox/cime/src/build_scripts/buildlib.mct FAILED, cat /cesm/scratch/mycasg.201231-203305

/usr/bin/ar: two different operation options specified
make[1]: *** [Makefile:55: libmpeu.a] Error 1
make: *** [/my_cesm_sandbox/cime/src/externals/mct/Makefile:10: subdirs] Error 2
 

MabelSue

MabelSue
New Member
Can you provide the information listed in the below link, including the files listed under the title "If this is a port to a new machine":

Information to include in help requests
Thanks for your help.Issues happened on cmd"./create_test --xml-category prealpha --xml-machine cheyenne --xml-compiler intel --machine centos7-linux --compiler gnu" during porting CESM to a cluster login node.

I guess I have two gcc environments. A virtual environment is builded,and they are not fixed correctly. I altered config_machines.xml in the directory Cime.You can see the attach files below.

Next,I will try on porting without virtual environment. I still wanna figure out the issues. Please help me,thanks!
______________________________________________________________________
Errors:
1.I have installed gcc g++,without gfortran:
..compilation aborted for /public/home/fshi/model/soft/CESM/my_cesm_sandbox/cime/src/externals/pio1/pio/pio_types.F90 (code 1)
make[3]: *** [pio/CMakeFiles/pio.dir/pio_types.F90.o] Error 1
make[2]: *** [pio/CMakeFiles/pio.dir/pio_types.F90.o.provides] Error 2
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [pio/CMakeFiles/pio.dir/all] Error 2

2.I have installed gcc_linux-64,gxx_linux-64,gfortran_linux-64 ( config.log )
..ERROR: configure: error: in `/wind1/home/19suy/cesm/scratch/sharedlibroot.20210111_103041_2lrqw1/gnu/openmpi/nodebug/nothreads/mct':
configure: error: C compiler cannot create executables
See `config.log' for more details
make: *** [/wind1/home/19suy/cesm/scratch/PEM.f19_g16_rx1.A.centos7-linux_gnu.20210111_103041_2lrqw1/Tools/Makefile:605: /wind1/home/19suy/cesm/scratch/sharedlibroot.20210111_103041_2lrqw1/gnu/openmpi/nodebug/nothreads/mct/Makefile.conf] Error 77
 

Attachments

  • version_info.txt
    5.9 KB · Views: 2

MabelSue

MabelSue
New Member
Can you provide the information listed in the below link, including the files listed under the title "If this is a port to a new machine":

Information to include in help requests
config.log

___________________________
..reference to `clogq@QUADMATH_1.0'
/wind1/home/19suy/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /wind1/home/19suy/anaconda3/envs/pyn_env/lib/./libgfortran.so.4: undefined reference to `lroundq@QUADMATH_1.0'
collect2: error: ld returned 1 exit status
configure:2426: $? = 1
configure:2464: result: no
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "MCT"
| #define PACKAGE_TARNAME "mct"
| #define PACKAGE_VERSION "2.8"
| #define PACKAGE_STRING "MCT 2.8"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h. */

______________________________


config_machines.xml

____________________________

<machine MACH="centos7-linux">
<DESC>
Example port to centos7 linux system with gcc, netcdf, pnetcdf and mpich
using modules from Environment Modules – A Great Tool for Clusters » ADMIN Magazine
</DESC>
<NODENAME_REGEX>login</NODENAME_REGEX>
<OS>LINUX</OS>
<PROXY> https://howto.get.out </PROXY>
<COMPILERS>intel,gnu</COMPILERS>
<MPILIBS>openmpi,mpich</MPILIBS>
<PROJECT>none</PROJECT>
<SAVE_TIMING_DIR> </SAVE_TIMING_DIR>
<CIME_OUTPUT_ROOT>$ENV{HOME}/cesm/scratch</CIME_OUTPUT_ROOT>
<DIN_LOC_ROOT>$ENV{HOME}/cesm/inputdata</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>$ENV{HOME}/cesm/inputdata/lmwg</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>$ENV{HOME}/cesm/archive/$CASE</DOUT_S_ROOT>
<BASELINE_ROOT>$ENV{HOME}/cesm/cesm_baselines</BASELINE_ROOT>
<CCSM_CPRNC>$ENV{HOME}/cesm/tools/cime/tools/cprnc/cprnc</CCSM_CPRNC>
<GMAKE>make</GMAKE>
<GMAKE_J>8</GMAKE_J>
<BATCH_SYSTEM>none</BATCH_SYSTEM>
<SUPPORTED_BY>me@my.address</SUPPORTED_BY>
<MAX_TASKS_PER_NODE>96</MAX_TASKS_PER_NODE>
<MAX_MPITASKS_PER_NODE>96</MAX_MPITASKS_PER_NODE>
<PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
<mpirun mpilib="default">
<executable>mpiexec</executable>
<arguments>
<arg name="ntasks"> --allow-run-as-root --mca btl ^openib -np {{ total_tasks }} </arg>
</arguments>
</mpirun>
<module_system type="module" allow_error="true">
<init_path lang="perl">/usr/share/Modules/init/perl.pm</init_path>
<init_path lang="python">/usr/share/Modules/init/python.py</init_path>
<init_path lang="csh">/usr/share/Modules/init/csh</init_path>
<init_path lang="sh">/usr/share/Modules/init/sh</init_path>
<cmd_path lang="perl">/usr/bin/modulecmd perl</cmd_path>
<cmd_path lang="python">/usr/bin/modulecmd python</cmd_path>
<cmd_path lang="sh">module</cmd_path>
<cmd_path lang="csh">module</cmd_path>
<modules>
<command name="purge"/>
</modules>
<modules compiler="gnu">
<command name="load">compiler/gnu/8.2.0</command>
<command name="load">mpi/3.3/gcc-8.2.0</command>
<command name="load">tool/netcdf/4.6.1/gcc-8.1.0</command>
</modules>
</module_system>
<environment_variables>
<env name="OMP_STACKSIZE">256M</env>
</environment_variables>
<resource_limits>
<resource name="RLIMIT_STACK">-1</resource>
</resource_limits>
</machine>
 

NeSe

NS
New Member
config.log

___________________________
..reference to `clogq@QUADMATH_1.0'
/wind1/home/19suy/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /wind1/home/19suy/anaconda3/envs/pyn_env/lib/./libgfortran.so.4: undefined reference to `lroundq@QUADMATH_1.0'
collect2: error: ld returned 1 exit status
configure:2426: $? = 1
configure:2464: result: no
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "MCT"
| #define PACKAGE_TARNAME "mct"
| #define PACKAGE_VERSION "2.8"
| #define PACKAGE_STRING "MCT 2.8"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h. */

______________________________


config_machines.xml

____________________________

<machine MACH="centos7-linux">
<DESC>
Example port to centos7 linux system with gcc, netcdf, pnetcdf and mpich
using modules from Environment Modules – A Great Tool for Clusters » ADMIN Magazine
</DESC>
<NODENAME_REGEX>login</NODENAME_REGEX>
<OS>LINUX</OS>
<PROXY> https://howto.get.out </PROXY>
<COMPILERS>intel,gnu</COMPILERS>
<MPILIBS>openmpi,mpich</MPILIBS>
<PROJECT>none</PROJECT>
<SAVE_TIMING_DIR> </SAVE_TIMING_DIR>
<CIME_OUTPUT_ROOT>$ENV{HOME}/cesm/scratch</CIME_OUTPUT_ROOT>
<DIN_LOC_ROOT>$ENV{HOME}/cesm/inputdata</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>$ENV{HOME}/cesm/inputdata/lmwg</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>$ENV{HOME}/cesm/archive/$CASE</DOUT_S_ROOT>
<BASELINE_ROOT>$ENV{HOME}/cesm/cesm_baselines</BASELINE_ROOT>
<CCSM_CPRNC>$ENV{HOME}/cesm/tools/cime/tools/cprnc/cprnc</CCSM_CPRNC>
<GMAKE>make</GMAKE>
<GMAKE_J>8</GMAKE_J>
<BATCH_SYSTEM>none</BATCH_SYSTEM>
<SUPPORTED_BY>me@my.address</SUPPORTED_BY>
<MAX_TASKS_PER_NODE>96</MAX_TASKS_PER_NODE>
<MAX_MPITASKS_PER_NODE>96</MAX_MPITASKS_PER_NODE>
<PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
<mpirun mpilib="default">
<executable>mpiexec</executable>
<arguments>
<arg name="ntasks"> --allow-run-as-root --mca btl ^openib -np {{ total_tasks }} </arg>
</arguments>
</mpirun>
<module_system type="module" allow_error="true">
<init_path lang="perl">/usr/share/Modules/init/perl.pm</init_path>
<init_path lang="python">/usr/share/Modules/init/python.py</init_path>
<init_path lang="csh">/usr/share/Modules/init/csh</init_path>
<init_path lang="sh">/usr/share/Modules/init/sh</init_path>
<cmd_path lang="perl">/usr/bin/modulecmd perl</cmd_path>
<cmd_path lang="python">/usr/bin/modulecmd python</cmd_path>
<cmd_path lang="sh">module</cmd_path>
<cmd_path lang="csh">module</cmd_path>
<modules>
<command name="purge"/>
</modules>
<modules compiler="gnu">
<command name="load">compiler/gnu/8.2.0</command>
<command name="load">mpi/3.3/gcc-8.2.0</command>
<command name="load">tool/netcdf/4.6.1/gcc-8.1.0</command>
</modules>
</module_system>
<environment_variables>
<env name="OMP_STACKSIZE">256M</env>
</environment_variables>
<resource_limits>
<resource name="RLIMIT_STACK">-1</resource>
</resource_limits>
</machine>
Were you able to resolve this problem? I am running into it as well.
 

NeSe

NS
New Member
Just closing the loop on this, I fixed it on my end by building Binutils from scratch and adding it to my paths rather than using the anaconda version.
 
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