Comments (6)
srtee
commented on August 23, 2024
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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from lammps-user-conp2.
XiaoboLinlin
commented on August 23, 2024
Thank you, Shern. It is working now after I deleted the two files. Btw, the cluster I am using is based on linux system.
from lammps-user-conp2.
srtee
commented on August 23, 2024
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
from lammps-user-conp2.
XiaoboLinlin
commented on August 23, 2024
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
from lammps-user-conp2.
Xiaohui-Yang
commented on August 23, 2024
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
from lammps-user-conp2.
srtee
commented on August 23, 2024
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
from lammps-user-conp2.
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