I have a question here on how a newly built GLIBC can be used from different machine.
I changed malloc code and compiled a local version of glibc
From : /home/1/glibc/puzzlebox/
Configure:**/eglibc-2.15/configure --prefix=/home/1/glibc/puzzlebox/lib32/ --host=i686-linux-gnu --build=i686-linux-gnu CC="gcc -m32 -g -ggdb -DMALLOC_DEBUG=1 -U__i686" CXX="g++ -m32 -g -ggdb -DMALLOC_DEBUG=1 -U __i686" CFLAGS="-O2 -march=i686 -U_FORTIFY_SOURCE -fno-stack-protector" CXXFLAGS="-O2 -march=i686 -U_FORTIFY_SOURCE -fno-stack-protector"
Make and install**: make clean;make;make install
Since my prefix is /home/1/glibc/puzzlebox/lib32/ , following directories are created under /home/1/glibc/puzzlebox/lib32/
bin etc include lib libexec sbin share
Now i copy library files /home/1/glibc/puzzlebox/lib32/lib/* to another repository /home/2/glibc/puzzlebox/lib32/lib
and pointed my gcc to use the library files from /home/2/glibc/puzzlebox/lib32/lib/* files
But i am getting the following error when compiling from
ld: cannot find /home/1/glibc/puzzlebox/lib32/lib/libc.so.6 inside
ld: cannot find /home/1/glibc/puzzlebox/lib32/lib/libc_nonshared.a inside
ld: cannot find /home/1/glibc/puzzlebox/lib32/lib/ld-linux.so.2 inside
collect2: error: ld returned 1 exit status
I am compilicc on /home/2 repository , but my glibc requires /home/1/glibc/puzzlebox/lib32/lib/libc.so.6
Is this because of static links? How can this be overcome? how can i build a glibc which can be used between repositories without rebuilding in each and every repository? and I dont want to override the already existing glibc so i dint use prefix as /usr
Please suggest!! Thanks in advance!!
Is this because of static links?
No. The most likely reason is that /home/2/glibc/puzzlebox/lib32/lib/libc.so (which is a linker script, i.e. a text file) has /home/1/glibc/puzzlebox/lib32/lib/libc.so.6 etc. in it.
You can edit that file, but really you should not compile GLIBC with --prefix=/foo unless that is where you intend to install it.
Related
I have inherited a Makefile which builds a .so file. It is linking with -lcrypto from OpenSSL on Ubuntu with gcc 4.7.4. Critically, it is NOT linking with -lssl nor -ldl, and when I run nm -g thelib.so, it only has the ~15 symbols from openssl crypto. However, they are all U (undefined).
I'm refactoring the Makefile on another Ubuntu machine. When I link with -lcrypto, it fails due to undefined symbols needed from dl. When I add linking to -ldl, those errors go away and linking succeeds. However, my .so file is 1.5 MB bigger than the original, and there are at least a hundred symbols related to SSL, which are all T (defined), which seem to indicate that -lssl is happening implicitly somehow.
While it would seem prudent and good that they are all defined in my case, I need to figure out how to produce the same result just as it is.
So, my question is, how does one get GCC to allow the linking of a .so file and accept undefined references? I've compared our commands, and there are little differences which I've tried to eliminate, but nothing seems to work. I read that it might be related to -Wl,--no-as-needed, but i'm using that. Here's my linker flags.
g++ -shared -o mylib.so myobjs.o -fPIC -lstdc++ -lm -z defs -Wl,-soname,mylib -Wl,--no-as-needed -lpthread -lcrypto -lz
On the other system (the one with the larger result), OpenSSL has apparently not been built as a shared object, only as a static library (but maybe as PIC, so that you can link the result into a shared object). You will have to install the packages that provide the shared object and the corresponding .so symbolic link.
I'm having some trouble building shared libraries from Ada packages without using GPR's.
I have a package, Numerics, in files "numerics.ads" and "numerics.adb". They have no dependencies. There is a small build script which does:
gnatmake -Os numerics.ad[bs] -cargs -fPIC
gcc -shared numerics.o -o libnumerics.so -Wl,-soname,libnumerics.so
The .so and .ali files are installed at /usr/lib, and the .ads file is installed at /usr/include.
gnatls -v outputs the following relevant parts:
Source Search Path:
<Current_Directory>
/usr/include
/usr/lib/gcc/x86_64-unknown-linux-gnu/5.1.0/adainclude
Object Search Path:
<Current_Directory>
/usr/lib
/usr/lib/gcc/x86_64-unknown-linux-gnu/5.1.0/adalib
So GNAT should have no problem finding the files.
Then, trying to compile a package that depends on Numerics:
gnatmake -O2 mathematics.ad[bs] -cargs -fPIC
outputs:
gcc -c -fPIC mathematics.adb
gcc -c -I./ -fPIC -I- /usr/include/numerics.ads
cannot generate code for file numerics.ads (package spec)
gnatmake: "/usr/include/numerics.ads" compilation error
This error has me thinking GNAT doesn't recognize the shared library, and is trying to rebuild Numerics.
I'd like to be building shared libraries, and only supply the spec for reference/documentation purposes.
edit:
So, it looks like gprbuild does two things I'm not doing. The first, is also passing -lnumerics to the compiler. The second, which shouldn't matter since libnumerics.so is in a standard directory anyways, is -L«ProjectDirectory». GPRbuild is obviously not doing desired behavior either, even though it's building the dependent project. It should be using the installed library /usr/lib/libnumerics.so, but instead is using «path»/Numerics/build/libnumerics.so. Furthermore, after building Numerics with GPRbuild, and then renaming the body to make it as if the body didn't exist (like with the installed files), when building Mathematics with GPRbuild, it complains about the exact same problem. It's as if the libraries aren't even shared, and GPRBuild is just making them look that way (except readelf reports the correct dependencies inside the libraries).
Adding -lnumerics to the build script accomplishes nothing; the build error is exactly the same. I'm completely lost at this point.
edit:
Following the link from Simon, the buildscript has changed to:
gnatmake -O2 mathematics.ad[bs] \
-aI/usr/include \
-aO/usr/lib \
-cargs -fPIC \
-largs -lnumerics
The error is essentially the same:
gcc -c -O2 -I/usr/include/ -fPIC mathematics.adb
gcc -c -I./ -O2 -I/usr/include/ -fPIC -I- /usr/include/numerics.ads
cannot generate code for file numerics.ads (package spec)
gnatmake: "/usr/include/numerics.ads" compilation error
I thought to check libnumerics.so is actually a correct shared library. ldd reports:
linux-vdso.so.1 (0x00007ffd944c1000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007f50d3927000)
/usr/lib64/ld-linux-x86-64.so.2 (0x00007f50d3ed4000)
So I'm thinking yes, the library is fine, and gnatmake still isn't recognizing it.
In general, you need to install the body of the packages as well (numerics.adb in your case). Also, I suspect you want to set the ALI files
(numerics.ali) as read-only, so that gnatmake does not try to recompile them.
I've installed GCC 3.4 to /opt/gcc-3.4, and I'm using it to compile legacy code which is incompatible with GCC 4. This also means old versions of the C(++) standard libraries, binutils, and utility libraries.
It works fine for some libraries, but fails when compiling libtiff, because it picks up the system libraries in /usr/lib (see output below). This might be an autotools/configure issue, but I'm not sure. I can't find a configure switch or environment variable, and I'd rather not modify my system /usr/lib/libc.so .
So how to make sure it links to the standard library in /opt/gcc-3.4.4/lib, and ignores /lib and /usr/lib completely?
Output of make (excerpt):
libtool: link: g++ -shared -nostdlib /usr/lib/crti.o /opt/gcc-3.4.3/lib/gcc/i686-pc-linux-gnu/3.4.3/crtbeginS.o .libs/tif_stream.o -Wl,--whole-archive ../port/.libs/libport.a -Wl,--no-whole-archive -Wl,-rpath -Wl,/home/jason/d0src34/prereq/tiff-3.9.4/libtiff/.libs -Wl,-rpath -Wl,/opt/gcc-3.4.3/lib -Wl,-rpath -Wl,/home/jason/d0src34/prereq/usr/lib -Wl,-rpath -Wl,/opt/gcc-3.4.3/lib ../libtiff/.libs/libtiff.so -L/usr/lib /usr/lib/libjpeg.so -lz -L/opt/gcc-3.4.3/lib/gcc/i686-pc-linux-gnu/3.4.3 -L/opt/gcc-3.4.3/lib/gcc/i686-pc-linux-gnu/3.4.3/../../.. /opt/gcc-3.4.3/lib/libstdc++.so -L/home/jason/Downloads/gcc-3.4.3/build/i686-pc-linux-gnu/libstdc++-v3/src -L/home/jason/Downloads/gcc-3.4.3/build/i686-pc-linux-gnu/libstdc++-v3/src/.libs -L/home/jason/Downloads/gcc-3.4.3/build/gcc -lm -lc -lgcc_s /opt/gcc-3.4.3/lib/gcc/i686-pc-linux-gnu/3.4.3/crtendS.o /usr/lib/crtn.o -Wl,-soname -Wl,libtiffxx.so.3 -o .libs/libtiffxx.so.3.9.4
/home/jason/d0src34/prereq/usr/bin/ld:/usr/lib/libc.so: file format not recognized; treating as linker script
/home/jason/d0src34/prereq/usr/bin/ld:/usr/lib/libc.so:5: parse error
I've found a (hackish) answer to my own question:
I've been using binutils 2.15, because later versions have an incompatibility with GCC 3.4. In more recent versions, the format of /usr/lib/libc.so has changed, and the old binutils can't parse it.
I temporarily commented out the last line (with "GROUP"), and my code compiled:
/* GNU ld script
Use the shared library, but some functions are only in
the static library, so try that secondarily. */
OUTPUT_FORMAT(elf32-i386)
/* GROUP ( /lib/libc.so.6 /usr/lib/libc_nonshared.a AS_NEEDED ( /lib/ld-linux.so.2 ) ) */
However, I'm not really satisfied, since I can hardly tell other people who want to use the code to edit their system files. Also, I'm not sure if I've linked it to the correct glibc version, since the system /usr/lib is still in the search path, so I can't tell for sure if the binaries will work on other systems.
I am trying to write a matlab mex function which uses libhdf5; My Linux install provides libhdf5-1.8 shared libraries and headers. However, my version of Matlab, r2007b, provides a libhdf5.so from the 1.6 release. (Matlab .mat files bootstrap hdf5, evidently). When I compile the mex, it segfaults in Matlab. If I downgrade my version of libhdf5 to 1.6 (not a long-term option), the code compiles and runs fine.
question: how do I solve this problem? how do I tell the mex compilation process to link against /usr/lib64/libhdf5.so.6 instead of /opt/matlab/bin/glnxa64/libhdf5.so.0 ? When I try to do this using -Wl,-rpath-link,/usr/lib64 in my compilation, I get errors like:
/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../x86_64-pc-linux-gnu/bin/ld: warning: libhdf5.so.0, needed by /opt/matlab/matlab75/bin/glnxa64/libmat.so, may conflict with libhdf5.so.6
/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: ld returned 1 exit status
mex: link of 'hdf5_read_strings.mexa64' failed.
make: *** [hdf5_read_strings.mexa64] Error 1
ack. the last resort would be to download a local copy of the hdf5-1.6.5 headers and be done with it, but this is not future proof (a Matlab version upgrade is in my future.). any ideas?
EDIT: per Ramashalanka's excellent suggestions, I
A) called mex -v to get the 3 gcc commands; the last is the linker command;
B) called that linker command with a -v to get the collect command;
C) called that collect2 -v -t and the rest of the flags.
The relevant parts of my output:
/usr/bin/ld: mode elf_x86_64
/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/crti.o
/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/crtbeginS.o
hdf5_read_strings.o
mexversion.o
-lmx (/opt/matlab/matlab75/bin/glnxa64/libmx.so)
-lmex (/opt/matlab/matlab75/bin/glnxa64/libmex.so)
-lhdf5 (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/libhdf5.so)
/lib64/libz.so
-lm (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/libm.so)
-lstdc++ (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/libstdc++.so)
-lgcc_s (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/libgcc_s.so)
/lib64/libpthread.so.0
/lib64/libc.so.6
/lib64/ld-linux-x86-64.so.2
-lgcc_s (/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/libgcc_s.so)
/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/crtendS.o
/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/../../../../lib64/crtn.o
So, in fact the libhdf5.so from /usr/lib64 is being referenced. However, this is being overriden, I believe, by the environment variable LD_LIBRARY_PATH, which my version of Matlab automagically sets at run-time so it can locate its own versions of e.g. libmex.so, etc.
I am thinking that the crt_file.c example works either b/c it does not use the functions I am using (H5DOpen, which had a signature change in the move from 1.6 to 1.8 (yes, I am using -DH5_USE_16_API)), or, less likely, b/c it does not hit the parts of Matlab internals that need hdf5. ack.
The following worked on my system:
Install hdf5 version 1.8.4 (you've already done this: I installed the source and compiled to ensure it is compatible with my system, that I get gcc versions and that I get the static libraries - e.g. the binaries offered for my system are icc specific).
Make a target file. You already have your own file. I used the simple h5_crtfile.c from here (a good idea to start with this simple file first a look for warnings). I changed main to mexFunction with the usual args and included mex.h.
Specify the static 1.8.4 library you want to load explicitly (the full path with no -L for it necessary) and don't include -lhdf5 in the LDFLAGS. Include a -t option so you can ensure that there is no dynamic hdf5 library being loaded. You also need -lz, with zlib installed. For darwin we also need a -bundle in LDFLAGS:
mex CFLAGS='-I/usr/local/hdf5/include' LDFLAGS='-t /usr/local/hdf5/lib/libhdf5.a -lz -bundle' h5_crtfile.c -v
For linux, you need an equivalent position-independent call, e.g. fPIC and maybe -shared, but I don't have a linux system with a matlab license, so I can't check:
mex CFLAGS='-fPIC -I/usr/local/hdf5/include' LDFLAGS='-t /usr/local/hdf5/lib/libhdf5.a -lz -shared' h5_crtfile.c -v
Run the h5_crtfile mex file. This runs without problems on my machine. It just does a H5Fcreate and H5Fclose to create "file.h5" in the current directory, and when I call file file.h5 I get file.h5: Hierarchical Data Format (version 5) data.
Note that if I include a -lhdf5 above in step 3, then matlab aborts when I try to run the executable (because it then uses matlab's dynamic libraries which for me are version 1.6.5), so this is definitely solving the problem on my system.
Thanks for the question. My solution above is definitely much easier for me than what I was doing before. Hopefully the above works for you.
I am accepting Ramashalanka's answer because it led me to the exact solution which I will post here for completeness only:
download the hdf5-1.6.5 library from the hdf5 website, and install the header files in a local directory;
tell mex to look for "hdf5.h" in this local directory, rather than in the standard location (e.g. /usr/include.)
tell mex to compile my code and the shared object library provided by matlab, and do not use the -ldfh5 flag in LDFLAGS.
the command I used is, essentially:
/opt/matlab/matlab_default/bin/mex -v CC#gcc CXX#g++ CFLAGS#"-Wall -O3 -fPIC -I./hdf5_1.6.5/src -I/usr/include -I/opt/matlab/matlab_default/extern/include" CXXFLAGS#"-Wall -O3 -fPIC -I./hdf5_1.6.5/src -I/usr/include -I/opt/matlab/matlab_default/extern/include " -O -lmwblas -largeArrayDims -L/usr/lib64 hdf5_read_strings.c /opt/matlab/matlab_default/bin/glnxa64/libhdf5.so.0
this gets translated by mex into the commands:
gcc -c -I/opt/matlab/matlab75/extern/include -DMATLAB_MEX_FILE -Wall -O3 -fPIC -I./hdf5_1.6.5/src -I/usr/include -I/opt/matlab/matlab_default/extern/include -O -DNDEBUG hdf5_read_strings.c
gcc -c -I/opt/matlab/matlab75/extern/include -DMATLAB_MEX_FILE -Wall -O3 -fPIC -I./hdf5_1.6.5/src -I/usr/include -I/opt/matlab/matlab_default/extern/include -O -DNDEBUG /opt/matlab/matlab75/extern/src/mexversion.c
gcc -O -pthread -shared -Wl,--version-script,/opt/matlab/matlab75/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined -o hdf5_read_strings.mexa64 hdf5_read_strings.o mexversion.o -lmwblas -L/usr/lib64 /opt/matlab/matlab_default/bin/glnxa64/libhdf5.so.0 -Wl,-rpath-link,/opt/matlab/matlab_default/bin/glnxa64 -L/opt/matlab/matlab_default/bin/glnxa64 -lmx -lmex -lmat -lm -lstdc++
this solution should work on all my various target machines and at least until I upgrade to matlab r2009a, which I believe uses hdf5-1.8. thanks for all the help, sorry for being so dense with this--I think I was overly-committed to using the packaged version of hdf5, rather than a local set of header files.
Note this would all have been trivial if Mathworks had provided a set of the header files with the Matlab distribution...
On my system, expat is located at
/usr/include/expat.h
/usr/include/expat_external.h
/usr/lib/libexpat.1.5.0.dylib
/usr/lib/libexpat.1.dylib
/usr/lib/libexpat.dylib
/usr/lib/libexpat.la
So I export the required variables for boost to build graphml
export EXPAT_INCLUDE=/usr/include
export EXPAT_LIBPATH=/usr/lib
then I run (where $DIR and $BOOST generate the paths I want the includes and libs to go)
./configure --includedir=$DIR/$BOOST --libdir=$DIR/$BOOST/lib \
--with-libraries=test,graph
I get this error:
ld: library not found for -lexpat collect2: ld returned 1 exit status
which boost says is caused by the line:
g++ -dynamiclib -install_name "libboost_graph-mt-1_35.dylib" -L"/usr/lib"
-o "bin.v2/libs/graph/build/darwin/release/macosx-version-10.4/threading-multi/libboost_graph-mt-1_35.dylib"
"bin.v2/libs/graph/build/darwin/release/macosx-version-10.4/threading-multi/read_graphviz_spirit.o"
"bin.v2/libs/graph/build/darwin/release/macosx-version-10.4/threading-multi/graphml.o"
-lexpat -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -Wl,-dead_strip -no_dead_strip_inits_and_terms
I don't get how it's not finding the expat library with -L"/usr/lib" and -lexpat as arguments? My understanding is that /usr/lib/libexpat.dylib is exactly referenced as -L"/usr/lib" and -lexpat.
The Jamfile for building graphml is here. If EXPAT_INCLUDE and EXPAT_LIBPATH aren't set then it warns you (lines 39-41 of jamfile)
warning: Graph library does not contain optional GraphML reader.
note: to enable GraphML support, set EXPAT_INCLUDE and
note: directories containing the Expat headers and libraries, respectively.
Another update:
I don't see an .so or a .a file in your list of where EXPAT is... doesn't that seem a bit strange? Normally it will create an alias for the library name
for example /usr/lib/libblah.so -> /usr/lib/libblaah.so.1.2
Is dynalib some Macintoshism (I don't use Macs much)
is .la the static version extension on this platform?
Update:
The quotes around the path seem troublesome...
-L"/usr/lib"
Try changing this to -L/usr/lib and -L /usr/lib
Older stuff:
The directive for the linker to include paths during the link step is -L. You need to look for some linker flags to update to include -L path_to_expat. I don't think the linker pays any attention to LD_LIBRARY_PATH. I am not sure what documentation you have read to set EXPAT_INCLUDE or EXPAT_LIBPATH.