Conda NNPDF package not setting PKG_CONFIG_PATH

[nhartland]

At least it seems like that on my machine.
I can't link to the conda libnnpdf because I can't see nnpdf.pc.

[nhartland]

Also happens if I make a specific conda dev environment.

[Zaharid]

Does conda install pkg-config fix it?

[nhartland]

Fixes not finding nnpdf.pc, yeah, but now it can't find libnnpdf at runtime.

dyld: Library not loaded: @rpath/libnnpdf.dylib
  Referenced from: /Users/hartland/work/code/nnpdfgit/apfelcomb/./apfel_comb
  Reason: image not found
[1]    29458 abort      ./apfel_comb app 10 160

[Zaharid]

You either have to point all the LDPATH like (whatever its called in mac) variables to point to the environment or install the conda compilers as per the vp guide. Second option being notably easier.

[nhartland]

install the conda compilers as per the vp guide

You mean as per the "Setting up a C++ development environment" section?
That's exactly what I'm doing:

→ conda activate nnpdf-dev
INFO: activate_clang_osx-64.sh made the following environmental changes:
+AR=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-ar
+AS=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-as
+CC=x86_64-apple-darwin13.4.0-clang
+CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe
+CHECKSYMS=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-checksyms
+CLANG=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-clang
+CODESIGN_ALLOCATE=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-codesign_allocate
+CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9
+DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra
+HOST=x86_64-apple-darwin13.4.0
+INDR=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-indr
+INSTALL_NAME_TOOL=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-install_name_tool
+LD=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-ld
+LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs
+LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs
+LIBTOOL=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-libtool
+LIPO=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-lipo
+NM=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-nm
+NMEDIT=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-nmedit
+OTOOL=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-otool
+PAGESTUFF=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-pagestuff
+RANLIB=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-ranlib
+REDO_PREBINDING=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-redo_prebinding
+SEGEDIT=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-segedit
+SEG_ADDR_TABLE=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-seg_addr_table
+SEG_HACK=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-seg_hack
+SIZE=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-size
+STRINGS=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-strings
+STRIP=/Users/hartland/miniconda3/envs/nnpdf-dev/bin/x86_64-apple-darwin13.4.0-strip
+_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
(nnpdf-dev) 
# hartland at Brian.local in ~/work/code/nnpdfgit/apfelcomb on git:master ✖︎ [23:54:14]
→ make clean && make > /dev/null
rm -f -f apfel_comb src/cfac_scale  appl_optgrid ftdy_hcx
rm -f -f fk_appl.o fk_dis.o  fk_qcd.o fk_utils.o fk_grids.o fk_ftdy.o ../libac_core.a
(nnpdf-dev) 
# hartland at Brian.local in ~/work/code/nnpdfgit/apfelcomb on git:master ✖︎ [23:54:35]
→ ./apfel_comb app 0 160
dyld: Library not loaded: @rpath/libnnpdf.dylib
  Referenced from: /Users/hartland/work/code/nnpdfgit/apfelcomb/./apfel_comb
  Reason: image not found
[1]    13505 abort      ./apfel_comb app 0 160
(nnpdf-dev) 

LDFLAGS doesn't appear to be pointing to anything useful, should it?

Edited to shorter version coming from outside the env

[nhartland]

Pointing LD_LIBRARY_PATH to the miniconda installation will obviously sort it out, but I thought that wasn't the idea here.

[Zaharid]

Remove CC= g++ LD= g++ from Makefile.inc in apfelcomb. These are set automatically.

…

On Tue, Feb 20, 2018 at 10:57 PM, Nathan Hartland ***@***.***> wrote: Pointing LD_LIBRARY_PATH to the miniconda installation will obviously sort it out, but I thought that wasn't the idea here. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#98 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFabUkhnRGGIVg6dRg_HqElJJgc6eryHks5tW03wgaJpZM4SMPF3> .

[nhartland]

Doesn't appear to make any difference. I should emphasise that this error happens at runtime, not compile time. The linking etc works perfectly well, my guess was that the LD flags for libnnpdf are not being exported properly.

[Zaharid]

Mmm make sure the Makefile is not overwriting the environment LDFLAGS but appending to them.

…

On Wed, Feb 21, 2018 at 10:19 AM, Nathan Hartland ***@***.***> wrote: Doesn't appear to make any difference. I should emphasise that this error happens at runtime, not compile time. The linking etc works perfectly well, my guess was that the LD flags for libnnpdf are not being exported properly. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#98 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFabUtPDz7SVaCGceJxSIqgHybTzq5I-ks5tW-2hgaJpZM4SMPF3> .

[nhartland]

Still no difference, the linker is still finding libnnpdf fine, it just can't find it at runtime.

I checked the trivial thing (appending the miniconda lib dir to LD_LIBRARY_PATHS) to be sure, and in this case it works fine, but naturally rather defeats the point of the development environment.

[nhartland]

(I say still no difference, what I mean is I changed the assignment of LDLIBS from = to += and it
made no difference. If I echo all the linker-related env variables before and after a make call, nothing is leaking).

[Zaharid]

Can you see if buildmaster works for you? apfelcomb certainly must work with the environment without other modifications than making sure the Makefile minds the environment.

[nhartland]

Good point:

→ ./buildmaster 
dyld: Library not loaded: @rpath/libnnpdf.dylib
  Referenced from: /Users/hartland/work/code/nnpdfgit/buildmaster/./buildmaster
  Reason: image not found
[1]    48534 abort      ./buildmaster

[Zaharid]

This is working fine on linux...

$ ldd buildmaster 
	linux-vdso.so.1 =>  (0x00007ffdde863000)
	libnnpdf.so => /home/zah/anaconda3/envs/nnpdf-dev/lib/libnnpdf.so (0x00007ffaa9a7b000)
	libgsl.so.19 => /home/zah/anaconda3/envs/nnpdf-dev/lib/libgsl.so.19 (0x00007ffaa9601000)
	libgslcblas.so.0 => /home/zah/anaconda3/envs/nnpdf-dev/lib/libgslcblas.so.0 (0x00007ffaa93ba000)
	libyaml-cpp.so.0.5 => /home/zah/anaconda3/envs/nnpdf-dev/lib/libyaml-cpp.so.0.5 (0x00007ffaa913f000)
	libstdc++.so.6 => /home/zah/anaconda3/envs/nnpdf-dev/lib/libstdc++.so.6 (0x00007ffaa8e05000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007ffaa8afc000)
	libgcc_s.so.1 => /home/zah/anaconda3/envs/nnpdf-dev/lib/libgcc_s.so.1 (0x00007ffaa88ea000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ffaa8520000)
	libLHAPDF.so => /home/zah/anaconda3/envs/nnpdf-dev/lib/libLHAPDF.so (0x00007ffaa8257000)
	libsqlite3.so.0 => /home/zah/anaconda3/envs/nnpdf-dev/lib/libsqlite3.so.0 (0x00007ffaa7f7f000)
	libarchive.so.13 => /home/zah/anaconda3/envs/nnpdf-dev/lib/libarchive.so.13 (0x00007ffaa7cc8000)
	/lib64/ld-linux-x86-64.so.2 (0x00007ffaa9fe2000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007ffaa7ac4000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007ffaa78a7000)
	libcrypto.so.1.0.0 => /home/zah/anaconda3/envs/nnpdf-dev/lib/./libcrypto.so.1.0.0 (0x00007ffaa7467000)
	liblzo2.so.2 => /home/zah/anaconda3/envs/nnpdf-dev/lib/./liblzo2.so.2 (0x00007ffaa7224000)
	liblz4.so.1 => /home/zah/anaconda3/envs/nnpdf-dev/lib/./liblz4.so.1 (0x00007ffaa7002000)
	libbz2.so.1.0 => /home/zah/anaconda3/envs/nnpdf-dev/lib/./libbz2.so.1.0 (0x00007ffaa6df0000)
	libxml2.so.2 => /home/zah/anaconda3/envs/nnpdf-dev/lib/./libxml2.so.2 (0x00007ffaa6a89000)
	libz.so.1 => /home/zah/anaconda3/envs/nnpdf-dev/lib/./libz.so.1 (0x00007ffaa6872000)
	liblzma.so.5 => /home/zah/anaconda3/envs/nnpdf-dev/lib/./liblzma.so.5 (0x00007ffaa664c000)
	libicuuc.so.58 => /home/zah/anaconda3/envs/nnpdf-dev/lib/././libicuuc.so.58 (0x00007ffaa629e000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007ffaa6096000)
	libicudata.so.58 => /home/zah/anaconda3/envs/nnpdf-dev/lib/./././libicudata.so.58 (0x00007ffaa4596000)

$ cat ~/anaconda3/envs/nnpdf-dev/lib/pkgconfig/nnpdf.pc 
prefix=/home/zah/anaconda3/envs/nnpdf-dev
exec_prefix=/home/zah/anaconda3/envs/nnpdf-dev
includedir=/home/zah/anaconda3/envs/nnpdf-dev/include
libdir=/home/zah/anaconda3/envs/nnpdf-dev/lib

Name: nnpdf
Description: The nnpdf library
Version: "1.2.0b5"
Cflags: -I/home/zah/anaconda3/envs/nnpdf-dev/include
Libs: -L/home/zah/anaconda3/envs/nnpdf-dev/lib -lnnpdf

Can you post what your pkg config file looks like?

[Zaharid]

Apart from posting the pkgconfig, could you run otool -L on buildmaster so we try to see what is going on.