Open ax3l opened 4 years ago
ax3l
commented
4 years ago I switched now to the new adios2::cxx11 and adios2::cxx11_mpi targets and get:
dyld: Library not loaded: @rpath/libadios2_cxx11.2.dylib
Referenced from: /Users/travis/build/bin/MyBinary
Reason: image not found@chuckatkins @bradking do you have an idea what's off on macOS? This one is a blocker for us to migrate to ADIOS 2.6.0 (and with it finalizing complex support for our users).
bradking
commented
4 years ago We need to figure out where that @rpath/ reference is coming from.
I use a spack-installed ADIOS 2.6.0
I just ran spack install adios2@2.6.0 on macOS and found that LC_ID_DYLIB in opt/spack/darwin-catalina-x86_64/clang-11.0.0-apple/adios2-2.6.0-ioxjevk4au455pt4rop2smac3kpcbgv5/lib/libadios2_cxx11.2.6.0.dylib is an absolute path and does not mention @rpath anywhere. Is that the case for yours too? You can find that file and run otool -l $file to see.
ax3l
commented
4 years ago Thanks, my libadios2_cxx11.2.dylib looks like this.
CI: https://travis-ci.com/github/openPMD/openPMD-api/jobs/349960561
/Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/adios2-2.6.0-62caxyc6a74de7kgb7e2l4w3obuhddtd/lib/libadios2_cxx11.2.dylib:
Mach header
magic cputype cpusubtype caps filetype ncmds sizeofcmds flags
0xfeedfacf 16777223 3 0x00 6 26 3200 0x00118085
Load command 0
cmd LC_SEGMENT_64
cmdsize 632
segname __TEXT
vmaddr 0x0000000000000000
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align 2^2 (4)
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Load command 1
cmd LC_SEGMENT_64
cmdsize 632
segname __DATA
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Load command 2
cmd LC_SEGMENT_64
cmdsize 72
segname __LINKEDIT
vmaddr 0x00000000000a5000
vmsize 0x0000000000095000
fileoff 671744
filesize 606656
maxprot 0x00000001
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Load command 3
cmd LC_ID_DYLIB
cmdsize 56
name @rpath/libadios2_cxx11.2.dylib (offset 24)
time stamp 1 Thu Jan 1 00:00:01 1970
current version 2.6.0
compatibility version 2.0.0
Load command 4
cmd LC_DYLD_INFO_ONLY
cmdsize 48
rebase_off 671744
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weak_bind_off 739296
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export_off 825104
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Load command 5
cmd LC_SYMTAB
cmdsize 24
symoff 912368
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stroff 992472
strsize 285928
Load command 6
cmd LC_DYSYMTAB
cmdsize 80
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Load command 7
cmd LC_UUID
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uuid 96AEDB87-7C94-3182-B541-C6BB463DD9D2
Load command 8
cmd LC_BUILD_VERSION
cmdsize 32
platform 1
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minos 10.14
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Load command 9
cmd LC_SOURCE_VERSION
cmdsize 16
version 0.0
Load command 10
cmd LC_LOAD_DYLIB
cmdsize 56
name @rpath/libadios2_core.2.dylib (offset 24)
time stamp 2 Thu Jan 1 00:00:02 1970
current version 2.6.0
compatibility version 2.0.0
Load command 11
cmd LC_LOAD_DYLIB
cmdsize 48
name /usr/lib/libc++.1.dylib (offset 24)
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compatibility version 1.0.0
Load command 12
cmd LC_LOAD_DYLIB
cmdsize 56
name /usr/lib/libSystem.B.dylib (offset 24)
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compatibility version 1.0.0
Load command 13
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0adios2-2.6.0-62caxyc6a74de7kgb7e2l4w3obuhddtd/lib (offset 12)
Load command 14
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0adios2-2.6.0-62caxyc6a74de7kgb7e2l4w3obuhddtd/lib64 (offset 12)
Load command 15
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/zstd-.4.5-7tsdvwjlqy33gyhfnnndtutehi6xxg2a/lib (offset 12)
Load command 16
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/libfabric-1.9.1-76anhiidtsbqlmfausybg7m3lqheyrq/lib (offset 12)
Load command 17
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/bzip2-1.0.8-tdq3ofob2xue6gkhp6pjphj7wldt4yl/lib (offset 12)
Load command 18
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/zlib-1.2.11-6m74cvmbqpza7ljfyle3ccmilsxyebe/lib (offset 12)
Load command 19
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/c-blosc-1.17.0-qqoaza5pizhtc7iojvxnzmj6rhg5vpp/lib (offset 12)
Load command 20
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/snappy-1.1.7-hduzhnbapqnnskr6hgfpe45t7k7sv2j/lib (offset 12)
Load command 21
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/lz4-1.9.2-wcj7r4347j3bfksp7nkyzj5zanszgpw/lib (offset 12)
Load command 22
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/libffi-3.3-l3xx7qvdynex6icppsprszz5z3jwjc4/lib (offset 12)
Load command 23
cmd LC_FUNCTION_STARTS
cmdsize 16
dataoff 908200
datasize 3936
Load command 24
cmd LC_DATA_IN_CODE
cmdsize 16
dataoff 912136
datasize 232
Load command 25
cmd LC_RPATH
cmdsize 32
path @loader_path/../lib (offset 12)@ax3l thanks. Your libadios2_cxx11.2.dylib indeed has LC_ID_DYLIB set to @rpath/libadios2_cxx11.2.dylib. That is different than on my machine's spack installation. Does spack have any options for that?
What did the adios2 .dylib files in ADIOS2 2.5 have for you?
ax3l
commented
4 years ago Thanks @bradking. In ADIOS2 2.5.0 the symbols looks like this: https://travis-ci.com/github/openPMD/openPMD-api/builds/172164002
/Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/adios2-2.5.0-sf6eyfn6xjlwvbvgs7dajgdpvs6ihrnb/lib/libadios2.2.dylib:
Mach header
magic cputype cpusubtype caps filetype ncmds sizeofcmds flags
0xfeedfacf 16777223 3 0x00 6 28 3864 0x00118085
Load command 0
cmd LC_SEGMENT_64
cmdsize 632
segname __TEXT
vmaddr 0x0000000000000000
vmsize 0x0000000000488000
fileoff 0
filesize 4751360
maxprot 0x00000005
initprot 0x00000005
nsects 7
flags 0x0
Section
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segname __TEXT
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offset 13184
align 2^4 (16)
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Section
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offset 4405968
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Section
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Section
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Section
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Section
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Section
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size 0x000000000000f278
offset 4689288
align 2^2 (4)
reloff 0
nreloc 0
flags 0x00000000
reserved1 0
reserved2 0
Load command 1
cmd LC_SEGMENT_64
cmdsize 712
segname __DATA
vmaddr 0x0000000000488000
vmsize 0x000000000000d000
fileoff 4751360
filesize 49152
maxprot 0x00000003
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Section
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Section
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Section
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Load command 2
cmd LC_SEGMENT_64
cmdsize 72
segname __LINKEDIT
vmaddr 0x0000000000495000
vmsize 0x0000000000194000
fileoff 4800512
filesize 1651412
maxprot 0x00000001
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nsects 0
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Load command 3
cmd LC_ID_DYLIB
cmdsize 168
name /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/adios2-2.5.0-sf6eyfn6xjlwvbvgs7dajgdpvs6ihrnb/lib/libadios2.2.dylib (offset 24)
time stamp 1 Thu Jan 1 00:00:01 1970
current version 2.5.0
compatibility version 2.0.0
Load command 4
cmd LC_DYLD_INFO_ONLY
cmdsize 48
rebase_off 4800512
rebase_size 752
bind_off 4801264
bind_size 3776
weak_bind_off 4805040
weak_bind_size 143816
lazy_bind_off 4948856
lazy_bind_size 12112
export_off 4960968
export_size 310616
Load command 5
cmd LC_SYMTAB
cmdsize 24
symoff 5286544
nsyms 14286
stroff 5526796
strsize 925128
Load command 6
cmd LC_DYSYMTAB
cmdsize 80
ilocalsym 0
nlocalsym 8090
iextdefsym 8090
nextdefsym 5832
iundefsym 13922
nundefsym 364
tocoff 0
ntoc 0
modtaboff 0
nmodtab 0
extrefsymoff 0
nextrefsyms 0
indirectsymoff 5515120
nindirectsyms 2919
extreloff 0
nextrel 0
locreloff 0
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Load command 7
cmd LC_UUID
cmdsize 24
uuid F533A1D5-FC81-3DBC-8760-11843D80C04B
Load command 8
cmd LC_BUILD_VERSION
cmdsize 32
platform 1
sdk 10.15
minos 10.14
ntools 1
tool 3
version 520.0
Load command 9
cmd LC_SOURCE_VERSION
cmdsize 16
version 0.0
Load command 10
cmd LC_LOAD_DYLIB
cmdsize 168
name /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/adios2-2.5.0-sf6eyfn6xjlwvbvgs7dajgdpvs6ihrnb/lib/libtaustubs.dylib (offset 24)
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compatibility version 0.0.0
Load command 11
cmd LC_LOAD_DYLIB
cmdsize 168
name /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/adios2-2.5.0-sf6eyfn6xjlwvbvgs7dajgdpvs6ihrnb/lib/libadios2_sst.2.dylib (offset 24)
time stamp 2 Thu Jan 1 00:00:02 1970
current version 2.5.0
compatibility version 2.0.0
Load command 12
cmd LC_LOAD_DYLIB
cmdsize 176
name /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/c-blosc-1.17.0-zqqoaza5pizhtc7iojvxnzmj6rhg5vpp/lib/libblosc.1.17.0.dylib (offset 24)
time stamp 2 Thu Jan 1 00:00:02 1970
current version 1.17.0
compatibility version 1.0.0
Load command 13
cmd LC_LOAD_DYLIB
cmdsize 48
name @rpath/libbz2.1.dylib (offset 24)
time stamp 2 Thu Jan 1 00:00:02 1970
current version 1.0.0
compatibility version 1.0.8
Load command 14
cmd LC_LOAD_DYLIB
cmdsize 48
name /usr/lib/libc++.1.dylib (offset 24)
time stamp 2 Thu Jan 1 00:00:02 1970
current version 800.7.0
compatibility version 1.0.0
Load command 15
cmd LC_LOAD_DYLIB
cmdsize 56
name /usr/lib/libSystem.B.dylib (offset 24)
time stamp 2 Thu Jan 1 00:00:02 1970
current version 1281.0.0
compatibility version 1.0.0
Load command 16
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/adios2-2.5.0-sf6eyfn6xjlwvbvgs7dajgdpvs6ihrnb/lib (offset 12)
Load command 17
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/adios2-2.5.0-sf6eyfn6xjlwvbvgs7dajgdpvs6ihrnb/lib64 (offset 12)
Load command 18
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/c-blosc-1.17.0-zqqoaza5pizhtc7iojvxnzmj6rhg5vpp/lib (offset 12)
Load command 19
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/libfabric-1.9.1-h76anhiidtsbqlmfausybg7m3lqheyrq/lib (offset 12)
Load command 20
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/snappy-1.1.7-ehduzhnbapqnnskr6hgfpe45t7k7sv2j/lib (offset 12)
Load command 21
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/libffi-3.3-znztsxzjr4rrkb6llnsp3wpwbvxzjn7a/lib (offset 12)
Load command 22
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/zlib-1.2.11-c6m74cvmbqpza7ljfyle3ccmilsxyebe/lib (offset 12)
Load command 23
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/lz4-1.9.2-ywcj7r4347j3bfksp7nkyzj5zanszgpw/lib (offset 12)
Load command 24
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/zstd-1.4.5-7tsdvwjlqy33gyhfnnndtutehi6xxg2a/lib (offset 12)
Load command 25
cmd LC_RPATH
cmdsize 136
path /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/bzip2-1.0.8-stdq3ofob2xue6gkhp6pjphj7wldt4yl/lib (offset 12)
Load command 26
cmd LC_FUNCTION_STARTS
cmdsize 16
dataoff 5271584
datasize 14016
Load command 27
cmd LC_DATA_IN_CODE
cmdsize 16
dataoff 5285600
datasize 944both use the same (latest) version of Spack to install.
bradking
commented
4 years ago @ax3l thanks. That ADIOS 2.5 library has LC_ID_DYLIB set to /Users/travis/.cache/spack/opt/spack/darwin-mojave-x86_64/clang-11.0.0/adios2-2.5.0-sf6eyfn6xjlwvbvgs7dajgdpvs6ihrnb/lib/libadios2.2.dylib which is expected and does not mention @rpath/.
It also matches what I see on my installations for ADIOS 2.5 and 2.6, which I installed on macOS in a brand new spack tree using spack install adios2@2.5.0 and spack install adios2@2.6.0. So the question remains: why does your spack-installed ADIOS2 2.6 use @rpath while mine does not? That is a question for a spack expert.
ax3l
commented
4 years ago Intriguing, thank you for testing this. Just to collect all data: which version of CMake did you use?
With CMake 3.12.0 I can reproduce this on macOS 10.13 (AppleClang 10.0) and 10.14 (AppleClang 11.0) on Travis-CI and set the following Spack configs: https://github.com/openPMD/openPMD-api/tree/3ff42bedbef2ab00457d26f5fd5f9d23dc7dcfe8/.github/ci/spack . None of them should be related to rpaths but I build ADIOS2 with the variant modifcations ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc.
This is the Spack CMake-related RPath info I can find in the docs:
Also inquired upstream.
There is the logic in build_environment.py to create SPACK_COMPILER_IMPLICIT_RPATHS, SPACK_COMPILER_EXTRA_RPATHS, SPACK_RPATH_DIRS, and SPACK_RPATH_DEPS. If you follow those you should see how they were constructed. If the library is pointing to itself, I would guess that is coming from SPACK_RPATH_DIRS or SPACK_RPATH_DEPS (someone forgot to exclude the root from a DAG traversal) or it could be the package itself.
bradking
commented
4 years ago I ran those spack install commands on macOS 10.15 with AppleClang 11.0. CMake 3.17.0 was in my PATH.
ax3l
commented
4 years ago Still had no time to debug this inside Spack, but will work-around this for now by building a adios2 ~shared ADIOS2 in our CI to keep going.
Now get an interesting Library not loaded: @rpath/libbz2.1.dylib when running an executable that links against the dynamic libopenPMD, which in turn was built against a static adios2. Will disable that as well via adios2 ~bzip2.
manauref
commented
2 years ago Any updates on this? Is the Mac python bindings not working/usable at the moment because of this? I haven't been able to install/use them.
williamfgc
commented
2 years ago @manauref in case you don't need the latest development, there is the adios2 brew package that @ax3l put together. Hope it helps.
Describe the bug I am currently transitioning to ADIOS 2.6.0 in our CI and encounter problems at runtime with the new split libraries on macOS 10.13 and 10.14 of the form:
To Reproduce I use a spack-installed ADIOS 2.6.0 and built against it with CMake. I run into issues as seen in: https://travis-ci.com/github/openPMD/openPMD-api/builds/170615793
We use the native C++11 API of ADIOS2. Other dependencies in our downstream
CMakeLists.txtmight activate the C language in CMake, but we do not use the ADIOS2 C bindings directly.Expected behavior Did build & run with ADIOS 2.5.0 :)
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