ljc-geo
commented
4 years ago Hi, I received your email. Thank you for bringing this to my attention.
First, let me ask you, do you have a working version of mpi installed. If you are trying to compile and use the inversion portion, this inversion executable needs to compile with 'mpicc' and needs access to the mpi libraries (the dev or devel packages).
Also, since the errors are quite long it would be helpful to capture them to a file and send me the file. When trying to read them, I feel some bits are missing. Could you do this?
Thanks, I will work on getting this to compile.
Cheers, Laura Connor Research Associate 813-334-0546 (mobile)
School of Geosciences University of South Florida Tampa, Florida 33620
From: CrystalShardz notifications@github.com Sent: Monday, August 10, 2020 6:27 AM To: geoscience-community-codes/tephra2 tephra2@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [geoscience-community-codes/tephra2] Unable to build (#1)
When attempting to run make as instructed this fails. See output below:
phil@B88A60FA4E7F:/mnt/c/users/phil/downloads/tephra2-master$ make cd inversion_src; make; cd .. make[1]: Entering directory '/mnt/c/users/phil/downloads/tephra2-master/inversion_src' which mpicc-Wall -O3 -idirafter ../include -c master.c /bin/sh: 1: -Wall: not found makefile:38: recipe for target 'master.o' failed make[1]: [master.o] Error 127 make[1]: Leaving directory '/mnt/c/users/phil/downloads/tephra2-master/inversion_src' cd forward_src; make; cd .. make[1]: Entering directory '/mnt/c/users/phil/downloads/tephra2-master/forward_src'which gcc-Wall -O3 -idirafter ../include -o tephra2-2012 new_tephra.o tephra2_calc.o -lm ../lib64/libgc.a -ldl /usr/bin/ld: ../lib64/libgc.a(malloc.o): relocation R_X86_64_32S against symbolGC_obj_kinds' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(mallocx.o): relocation R_X86_64_32S against symbol GC_obj_kinds' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(alloc.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(reclaim.o): relocation R_X86_64_32S against undefined symbol GC_leaked' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(allchblk.o): relocation R_X86_64_32S against symbol GC_hblkfreelist' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(misc.o): relocation R_X86_64_32S against undefined symbol GC_arrays' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(os_dep.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(mark_rts.o): relocation R_X86_64_32S against undefined symbol GC_arrays' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(headers.o): relocation R_X86_64_32S against undefined symbol GC_arrays' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(mark.o): relocation R_X86_64_32 against .text' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(obj_map.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(blacklst.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(finalize.o): relocation R_X86_64_32S against .bss' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(new_hblk.o): relocation R_X86_64_32S against symbol GC_obj_kinds' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(dyn_load.o): relocation R_X86_64_32 against symbol dl_iterate_phdr@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(mach_dep.o): relocation R_X86_64_32 against symbol `GC_push_current_stack' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: final link failed: Nonrepresentable section on output collect2: error: ld returned 1 exit status makefile:29: recipe for target 'tephra2-2012' failed make[1]: [tephra2-2012] Error 1 make[1]: Leaving directory '/mnt/c/users/phil/downloads/tephra2-master/forward_src'
Please can you advise how this can be resolved? This is running under Ubuntu 18.04.4 LTS
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgeoscience-community-codes%2Ftephra2%2Fissues%2F1&data=02%7C01%7Clconnor%40usf.edu%7C27b3c3f6e17346d1ee9b08d83d180063%7C741bf7dee2e546df8d6782607df9deaa%7C0%7C0%7C637326520578902271&sdata=5gAQ8fWNiBCwTYPND4wDAt%2BGPZqEXHredtoUImAW2Xk%3D&reserved=0, or unsubscribehttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FABF6GGFWZ2LAGNRHJLHEGCDR77DPZANCNFSM4PZ2AKQQ&data=02%7C01%7Clconnor%40usf.edu%7C27b3c3f6e17346d1ee9b08d83d180063%7C741bf7dee2e546df8d6782607df9deaa%7C0%7C0%7C637326520578902271&sdata=tpWBQoPZcAKCayTE9zpFs5rZUfQcynCLC51UnAcsf0c%3D&reserved=0.
[EXTERNAL EMAIL] DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.
CrystalShardz
When attempting to run make as instructed this fails. See output below:
phil@B88A60FA4E7F:/mnt/c/users/phil/downloads/tephra2-master$ make cd inversion_src; make; cd .. make[1]: Entering directory '/mnt/c/users/phil/downloads/tephra2-master/inversion_src'which mpicc-Wall -O3 -idirafter ../include -c master.c /bin/sh: 1: -Wall: not found makefile:38: recipe for target 'master.o' failed make[1]: *** [master.o] Error 127 make[1]: Leaving directory '/mnt/c/users/phil/downloads/tephra2-master/inversion_src' cd forward_src; make; cd .. make[1]: Entering directory '/mnt/c/users/phil/downloads/tephra2-master/forward_src'which gcc-Wall -O3 -idirafter ../include -o tephra2-2012 new_tephra.o tephra2_calc.o -lm ../lib64/libgc.a -ldl /usr/bin/ld: ../lib64/libgc.a(malloc.o): relocation R_X86_64_32S against symbolGC_obj_kinds' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(mallocx.o): relocation R_X86_64_32S against symbolGC_obj_kinds' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(alloc.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(reclaim.o): relocation R_X86_64_32S against undefined symbolGC_leaked' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(allchblk.o): relocation R_X86_64_32S against symbolGC_hblkfreelist' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(misc.o): relocation R_X86_64_32S against undefined symbolGC_arrays' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(os_dep.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(mark_rts.o): relocation R_X86_64_32S against undefined symbolGC_arrays' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(headers.o): relocation R_X86_64_32S against undefined symbolGC_arrays' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(mark.o): relocation R_X86_64_32 against.text' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(obj_map.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(blacklst.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(finalize.o): relocation R_X86_64_32S against.bss' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(new_hblk.o): relocation R_X86_64_32S against symbolGC_obj_kinds' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(dyn_load.o): relocation R_X86_64_32 against symboldl_iterate_phdr@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../lib64/libgc.a(mach_dep.o): relocation R_X86_64_32 against symbol `GC_push_current_stack' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: final link failed: Nonrepresentable section on output collect2: error: ld returned 1 exit status makefile:29: recipe for target 'tephra2-2012' failed make[1]: *** [tephra2-2012] Error 1 make[1]: Leaving directory '/mnt/c/users/phil/downloads/tephra2-master/forward_src'Please can you advise how this can be resolved? This is running under Ubuntu 18.04.4 LTS