Compiling error in Cluster
XiaoboLinlin opened this issue · comments
Hi Shern,
I am having compiling error like this.
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp: In member function 'void LAMMPS_NS::PPPMCONPIntel::elyte_make_rho(LAMMPS_NS::IntelBuffers<flt_t, acc_t>*)':
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:309:18:error: 'nlocal' has not been declared
shared(nthr, nlocal, global_elyte_density) if(!_use_lrt)
^~~~~~
In file included from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/intel_buffers.h:27:0,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/fix_intel.h:28,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/pppm_intel.h:31,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.h:28,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:19:
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:415:51:error: 'thr' was not declared in this scope
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/intel_preprocess.h:167:23: note: in definition of macro 'IP_PRE_omp_range'
int idelta = inum/nthreads; \
^~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:415:7: note: in expansion of macro 'IP_PRE_omp_range_id'
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^~~~~~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:415:51:note: suggested alternative: 'nthr'
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/intel_preprocess.h:167:23: note: in definition of macro 'IP_PRE_omp_range'
int idelta = inum/nthreads; \
^~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:415:7: note: in expansion of macro 'IP_PRE_omp_range_id'
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^~~~~~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp: In member function 'void LAMMPS_NS::PPPMCONPIntel::ele_make_rho(LAMMPS_NS::IntelBuffers<flt_t, acc_t>*)':
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:499:18:error: 'nlocal' has not been declared
shared(nthr, nlocal, global_ele_density) if(!_use_lrt)
^~~~~~
In file included from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/intel_buffers.h:27:0,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/fix_intel.h:28,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/pppm_intel.h:31,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.h:28,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:19:
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:567:51:error: 'thr' was not declared in this scope
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/intel_preprocess.h:167:23: note: in definition of macro 'IP_PRE_omp_range'
int idelta = inum/nthreads; \
^~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:567:7: note: in expansion of macro 'IP_PRE_omp_range_id'
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^~~~~~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:567:51:note: suggested alternative: 'nthr'
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/intel_preprocess.h:167:23: note: in definition of macro 'IP_PRE_omp_range'
int idelta = inum/nthreads; \
^~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:567:7: note: in expansion of macro 'IP_PRE_omp_range_id'
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^~~~~~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp: In member function 'void LAMMPS_NS::PPPMCONPIntel::ele_make_rho(LAMMPS_NS::IntelBuffers<flt_t, acc_t>*) [with flt_t = float; acc_t = double]':
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:524:24:error: 'ele2tag' not specified in enclosing 'parallel'
int i = atom->map(ele2tag[iele]);
~~~~~~~~~^~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:498:11:error: enclosing 'parallel'
#pragma omp parallel LMP_DEFAULT_NONE \
^~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp: In member function 'void LAMMPS_NS::PPPMCONPIntel::ele_make_rho(LAMMPS_NS::IntelBuffers<flt_t, acc_t>*) [with flt_t = double; acc_t = double]':
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:524:24:error: 'ele2tag' not specified in enclosing 'parallel'
int i = atom->map(ele2tag[iele]);
~~~~~~~~~^~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:498:11:error: enclosing 'parallel'
#pragma omp parallel LMP_DEFAULT_NONE \
^~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp: In member function 'void LAMMPS_NS::PPPMCONPIntel::ele_make_rho(LAMMPS_NS::IntelBuffers<flt_t, acc_t>*) [with flt_t = float; acc_t = float]':
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:524:24:error: 'ele2tag' not specified in enclosing 'parallel'
int i = atom->map(ele2tag[iele]);
~~~~~~~~~^~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:498:11:error: enclosing 'parallel'
#pragma omp parallel LMP_DEFAULT_NONE \
^~~
gmake[2]: *** [CMakeFiles/lammps.dir/build.make:8751: CMakeFiles/lammps.dir/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp.o] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:1003: CMakeFiles/lammps.dir/all] Error 2
gmake: *** [Makefile:130: all] Error 2
Any suggests for this? looks like something error in parallel. (I installed USER_INTEL as you said)
Best,
Xiaobo
Hi,
I'm not sure what the issue might be -- those compile fine across various servers that I use. I am not sure if the USER-INTEL package works on Macs. It is probably better to disable those two files (just delete them from the source directory) and keep going.
All the best,
Shern
…---------------------------------
Dr Shern Tee
Postdoctoral Research Fellow
Australian Institute for Bioengineering and Nanotechnology
The University of Queensland
Brisbane Qld 4072 Australia
M +61 467 095 347
E ***@***.******@***.***>
CRICOS 00025B
[cid:7ec3187b-05cc-4883-883f-47a7f1077e04]
________________________________
From: XiaoboLinlin ***@***.***>
Sent: 11 May 2021 13:20
To: srtee/lammps-USER-CONP2 ***@***.***>
Cc: Subscribed ***@***.***>
Subject: [srtee/lammps-USER-CONP2] Compiling error in Cluster (#13)
Hi Shern,
I am having compiling error like this.
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp: In member function 'void LAMMPS_NS::PPPMCONPIntel::elyte_make_rho(LAMMPS_NS::IntelBuffers<flt_t, acc_t>*)':
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:309:18:error: 'nlocal' has not been declared
shared(nthr, nlocal, global_elyte_density) if(!_use_lrt)
^~~~~~
In file included from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/intel_buffers.h:27:0,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/fix_intel.h:28,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/pppm_intel.h:31,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.h:28,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:19:
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:415:51:error: 'thr' was not declared in this scope
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/intel_preprocess.h:167:23: note: in definition of macro 'IP_PRE_omp_range'
int idelta = inum/nthreads; \
^~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:415:7: note: in expansion of macro 'IP_PRE_omp_range_id'
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^~~~~~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:415:51:note: suggested alternative: 'nthr'
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/intel_preprocess.h:167:23: note: in definition of macro 'IP_PRE_omp_range'
int idelta = inum/nthreads; \
^~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:415:7: note: in expansion of macro 'IP_PRE_omp_range_id'
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^~~~~~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp: In member function 'void LAMMPS_NS::PPPMCONPIntel::ele_make_rho(LAMMPS_NS::IntelBuffers<flt_t, acc_t>*)':
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:499:18:error: 'nlocal' has not been declared
shared(nthr, nlocal, global_ele_density) if(!_use_lrt)
^~~~~~
In file included from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/intel_buffers.h:27:0,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/fix_intel.h:28,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/pppm_intel.h:31,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.h:28,
from /global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:19:
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:567:51:error: 'thr' was not declared in this scope
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/intel_preprocess.h:167:23: note: in definition of macro 'IP_PRE_omp_range'
int idelta = inum/nthreads; \
^~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:567:7: note: in expansion of macro 'IP_PRE_omp_range_id'
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^~~~~~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:567:51:note: suggested alternative: 'nthr'
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/USER-INTEL/intel_preprocess.h:167:23: note: in definition of macro 'IP_PRE_omp_range'
int idelta = inum/nthreads; \
^~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:567:7: note: in expansion of macro 'IP_PRE_omp_range_id'
IP_PRE_omp_range_id(ifrom, ito, tid, ngrid, thr);
^~~~~~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp: In member function 'void LAMMPS_NS::PPPMCONPIntel::ele_make_rho(LAMMPS_NS::IntelBuffers<flt_t, acc_t>*) [with flt_t = float; acc_t = double]':
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:524:24:error: 'ele2tag' not specified in enclosing 'parallel'
int i = atom->map(ele2tag[iele]);
~~~~~~~~~^~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:498:11:error: enclosing 'parallel'
#pragma omp parallel LMP_DEFAULT_NONE \
^~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp: In member function 'void LAMMPS_NS::PPPMCONPIntel::ele_make_rho(LAMMPS_NS::IntelBuffers<flt_t, acc_t>*) [with flt_t = double; acc_t = double]':
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:524:24:error: 'ele2tag' not specified in enclosing 'parallel'
int i = atom->map(ele2tag[iele]);
~~~~~~~~~^~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:498:11:error: enclosing 'parallel'
#pragma omp parallel LMP_DEFAULT_NONE \
^~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp: In member function 'void LAMMPS_NS::PPPMCONPIntel::ele_make_rho(LAMMPS_NS::IntelBuffers<flt_t, acc_t>*) [with flt_t = float; acc_t = float]':
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:524:24:error: 'ele2tag' not specified in enclosing 'parallel'
int i = atom->map(ele2tag[iele]);
~~~~~~~~~^~~~~~~~~~~~~~~
/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp:498:11:error: enclosing 'parallel'
#pragma omp parallel LMP_DEFAULT_NONE \
^~~
gmake[2]: *** [CMakeFiles/lammps.dir/build.make:8751: CMakeFiles/lammps.dir/global/project/projectdirs/m1046/Xiaobo/installed_software/lammps/src/pppm_conp_intel.cpp.o] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:1003: CMakeFiles/lammps.dir/all] Error 2
gmake: *** [Makefile:130: all] Error 2
Any suggests for this? looks like something error in parallel. (I installed USER_INTEL as you said)
Best,
Xiaobo
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Thank you, Shern. It is working now after I deleted the two files. Btw, the cluster I am using is based on linux system.
Hi Xiaobo,
Could you try compiling the pppm_conp_intel files with "-D BUILD_OMP=no"? Also, could you let me know what compiler and version number you are using?
Thanks,
Shern
Hi Xiaobo,
Could you try compiling the pppm_conp_intel files with "-D BUILD_OMP=no"? Also, could you let me know what compiler and version number you are using?
Thanks,
Shern
It is working using your flag! My compiler is GNU 8.3.0
Hi Shern,
Thank you for developing this code! Unfortunately, I have the same problem as Xiaobo, I use Intel compiler and intelmpi, but I cannot fix this problem by adding the "-D BUILD_OMP=no" flag...
All I can do is remove these two files (i.e., pppm_conp_intel.* ) and recompile the lammps again. My lammps version is 8 Apr 2021. However, the program failed when calculating the matrix, then end up with many core.* files.
Could you please give me some suggestions?
Thanks a lot for your help.
Cheers,
Xiaohui
Hi Xiaohui!
Could you open a new issue and tell me more about what system you are building on, and what compilers and compiler options you used?
Thanks!
Shern