Trying to install FFTW and feel like I have been going in circles. I need it for an R package (poisbinom) and I think I have it installed right (I'm on a cluster and don't have sudo privileges. I followed the instructions here: http://micro.stanford.edu/wiki/Install_FFTW3 )
The problem I'm running into is this:
g++ -std=gnu++14 -shared -L/usr/local/lib64 -o poisbinom.so RcppExports.o init.o poisbinom.o -lfftw3 -lm
/usr/bin/ld: cannot find -lfftw3
collect2: error: ld returned 1 exit status
I have a feeling it is because I did not install FFTW under usr/local/lib64, its under $HOME/usr/. My R install is under $HOME/R/lib64/R. I am not sure what variable to change to make it look in the right place, as I cant change this g++ call as it is part of an R install.packages call. I've been going in circles with this for two days now. Let me know if theres anything else I can provide to help.
I already ran install.packages("fftw") and that was successful and used LFFTW3 without issue because it looked in the right place. I mostly just need to know if I can point this gcc call to the right folder with an environment variable or something.
In case you have pkg-config on your system and your installation produced the required configuration files (e.g. fftw3.pc): Define the environment variable PKG_CONFIG_PATH to (also) include the directory with these configuration files for FFTW3.
Otherwise, you can define FFTW_CFLAGS and FFTW_LIBS:
fftw$ ./configure --help
[...]
FFTW_CFLAGS C compiler flags for FFTW, overriding pkg-config
FFTW_LIBS linker flags for FFTW, overriding pkg-config
[...]
I ended up having to add the variables to my bashrc file:
export PATH=$HOME/fftw_folder/bin:$PATH
export LD_LIBRARY_PATH=$HOME/fftw_folder/lib:$LD_LIBRARY_PATH
export LIBRARY_PATH=$HOME/fftw_folder/lib:$LIBRARY_PATH
export PKG_CONFIG_PATH=$HOME/_folder/lib/pkgconfig:$PKG_CONFIG_PATH
As laid out here: http://hpc.loni.org/docs/faq/installation-details.php
And now things seem to be moving forward smoothly. Thanks for the help!
Related
I'd like to learn how to write PNG images pixel-by-pixel using both RGB and HSV color models with C++. I read that this should be fairly easy using PNGwriter (https://github.com/pngwriter/pngwriter), but I've spent many hours struggling with installing it (on Ubuntu) and compiling my code with it. Any help would be much appreciated.
Disclaimer: I have a weird background in the sense that I have many years of experience in using Unix-like operating systems, doing stuff in the terminal, and writing code, but I know little/nothing about installing software from the source code or compiling programs manually or with makefiles from multiple source code files.
The installation instructions on GitHub advise to do one of the following:
Spack:
spack install pngwriter
spack load pngwriter
From Source:
First install the dependencies zlib, libpng, and (optional for text support) freetype. PNGwriter >can then be installed using CMake:
git clone https://github.com/pngwriter/pngwriter.git
mkdir -p pngwriter-build
cd pngwriter-build
# for own install prefix append: -DCMAKE_INSTALL_PREFIX=$HOME/somepath
cmake ../pngwriter
make -j
# optional
make test
# sudo is only required for system paths
sudo make install
I managed to install Spack and then PNGwriter, but couldn't compile the simplest program with it and wasn't able to figure out why. I then installed PNGwriter manually, but still couldn't compile anything with it. This was many hours of struggling ago so I, unfortunately, don't remember what kind of errors or problems I was encountering at this point.
The instructions on GitHub say the following about linking:
First set the following environment hint if PNGwriter was not installed in a system path:
# optional: only needed if installed outside of system paths
export CMAKE_PREFIX_PATH=$HOME/somepath:$CMAKE_PREFIX_PATH
Use the following lines in your projects CMakeLists.txt:
find_package(PNGwriter 0.7.0)
if(PNGwriter_FOUND)
target_link_libraries(YourTarget PRIVATE PNGwriter::PNGwriter)
endif(PNGwriter_FOUND)
Questions: How do I know if PNGwriter was or wasn't installed in a system path? I have libPNGwriter.a in /usr/local/lib and pngwriter.h in /usr/local/include --- does this mean that it was installed in a system path? When installing I simply tried to follow the instructions above. Do I just type the environment hint to the terminal or add it to some file? If the former then does it need to be given every time I open a new terminal session? Is "somepath" /usr/local/lib, /usr/local/include or something else?
Questions: Does the second part regarding "CMakeLists.txt" depend on whether PNGwriter was installed in a system path? What is "CMakeLists.txt"? I assume it's some file one's IDE creates, but my NetBeans projects don't seem to contain such files. What if I have a single source file and compile it manually in the terminal?
Now, let's say I'd like to compile the PNGwriter quickstart example:
#include <pngwriter.h>
int main()
{
int i;
int y;
pngwriter png(300, 300, 0, "test.png");
for(i = 1; i ≤ 300; i++)
{
y = 150 + 100*sin((double)i*9/300.0);
png.plot(i, y, 0.0, 0.0, 1.0);
}
png.close();
return 0;
}
The PNGwriter manual instructs to compile as
g++ myprogram.cc -o my_program `freetype-config --cflags` -I/usr/local/include -L/usr/local/lib -lpng -lpngwriter -lz -lfreetype
but I get errors
$ g++ example.cpp -o example `freetype-config --cflags` -I/usr/local/include -L/usr/local/lib -lpng -lpngwriter -lz -lfreetype
Package freetype2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `freetype2.pc'
to the PKG_CONFIG_PATH environment variable
Package 'freetype2', required by 'virtual:world', not found
Package freetype2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `freetype2.pc'
to the PKG_CONFIG_PATH environment variable
Package 'freetype2', required by 'virtual:world', not found
Package freetype2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `freetype2.pc'
to the PKG_CONFIG_PATH environment variable
Package 'freetype2', required by 'virtual:world', not found
Package freetype2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `freetype2.pc'
to the PKG_CONFIG_PATH environment variable
Package 'freetype2', required by 'virtual:world', not found
sed: -e expression #1, char 0: no previous regular expression
sed: -e expression #1, char 0: no previous regular expression
In file included from example.cpp:1:0:
/usr/local/include/pngwriter.h:66:22: fatal error: ft2build.h: No such file or directory
compilation terminated.
The answer to this Stack Overflow question (Trying to install pygame on ubuntu which gives error) suggests to install libfreetype6-dev, but I apparently have the latest version already whereby the errors remain unchanged. If I instead actually add the directory containing freetype2.pc (I found it by going to / and using find -name "freetype2.pc") to the environment variable (added export PKG_CONFIG_PATH="/usr/lib/x86_64-linux-gnu/pkgconfig/:$PKG_CONFIG_PATH to ~/.bashrc and did source ~/.bashrc) then I get new errors
$ g++ example.cpp -o example `freetype-config --cflags` -I/usr/local/include -L/usr/local/lib -lpng -lpngwriter -lz -lfreetype
/usr/bin/ld: cannot find -lpngwriter
collect2: error: ld returned 1 exit status
Here I figured out that I needed to replace -lpngwriter with -lPNGwriter (i.e., the manual is erroneous). Then I get:
$ g++ example.cpp -o example `freetype-config --cflags` -I/usr/local/include -L/usr/local/lib -lpng -lPNGwriter -lz -lfreetype
/usr/bin/ld: /usr/local/lib/libPNGwriter.a(pngwriter.cc.o): undefined reference to symbol 'png_set_sig_bytes##PNG12_0'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libpng.so: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
This is where I'm currently stuck. I can't seem to find a solution by googling (at least one that I'd understand).
Question: How do I get this working? How do I get it working in NetBeans? Do I get these problems because I effed up the linking step above?
Edit1: As per john's comment, I tried swapping -lpng and -lPNGwriter and I again get new errors:
$ g++ example.cpp -o example `freetype-config --cflags` -I/usr/local/include -L/usr/local/lib -lPNGwriter -lpng -lz -lfreetype
/usr/local/lib/libPNGwriter.a(pngwriter.cc.o): In function `pngwriter::close()':
pngwriter.cc:(.text+0x41c2): undefined reference to `png_convert_to_rfc1123_buffer'
/usr/local/lib/libPNGwriter.a(pngwriter.cc.o): In function `pngwriter::read_png_info(_IO_FILE*, png_struct_def**, png_info_def**)':
pngwriter.cc:(.text+0x4fdf): undefined reference to `png_set_longjmp_fn'
collect2: error: ld returned 1 exit status
I'm still left clueless.
Thanks to john, I think I got it figured out. My guess is that the installation from the source (after the Spack installation) messed things up somehow. I reinstalled PNGwriter using Spack and, now apparently having all the pieces for the compilation command, was finally able to compile the example code.
Summary:
Source Spack
# For bash/zsh/sh
$ . spack/share/spack/setup-env.sh
# For tcsh/csh
$ source spack/share/spack/setup-env.csh
# For fish
$ . spack/share/spack/setup-env.fish
Install using Spack (skip if already installed)
spack install pngwriter
Load PNGwriter (I guess one needs to do this in every new terminal session)
spack load pngwriter
Compile (note that this isn't quite what the PNGwriter manual suggests)
g++ example.cpp -o example `freetype-config --cflags` -I/usr/local/include -L/usr/local/lib -lPNGwriter -lpng -lz -lfreetype
I am trying to setup Coin-CLP that supports also CPLEX (which I have installed and is running smoothly on my machine) following the instructions found on the website.
Unfortunately when I try to run the configure step on the installation, that in my version where I want to include CPLEX as well looks like this:
./configure --with-cplex \
--with-cplex-lib="-L/opt/ibm/ILOG/CPLEX_Studio127/cplex/lib/x86-64_linux/static_pic -lilocplex -lconcert -lcplex -lm -lpthread" \
--with-cplex-incdir="/opt/ibm/ILOG/CPLEX_Studio127/cplex/include/ilcplex" \
--enable-static -C
I receive the following error:
checking whether symbol CPXgetstat is available with CPX... no
configure: error: Cannot find symbol(s) CPXgetstat with CPX
configure: error: /bin/bash './configure' failed for Osi
I have tried to search online and find similar issues and proposed solutions, but unfortunately so far I haven't managed to find any way to fix this.
So, any help would be really appreciated!
I've recently stumbled against this same issue trying to enable Fast-Downward planner to work with LP capabilities. I know this is an old question, but it is one of the few pages that show up when searching for this error, so I thought I may as well give my solution for it.
After digging through the config.log file inside the Osi folder, I found that there were undefined references to the functions from the DL (Dynamically Loaded) library, such as dlopen. So I added -ldl to the --with-cplex-lib configure argument. My configure call was like this at the end:
./configure CC="gcc" CFLAGS="-m64 -pthread -Wno-long-long" CXX="g++" \
CXXFLAGS="-m64 -pthread -Wno-long-long" LDFLAGS="-L$DOWNWARD_CPLEX_ROOT64/lib/x86-64_linux/static_pic/"\
--without-lapack --enable-static=yes --prefix="/usr/local/" --disable-zlib --disable-bzlib\
--with-cplex-incdir=$DOWNWARD_CPLEX_ROOT64/include/ilcplex --with-cplex-lib="-lcplex -lm -ldl"
Hope it helps.
I am trying to compile as this :
-bash-4.1$ g++ -static -m32 Hello.cpp
and getting errors like this:
/opt/rh/devtoolset-4/root/usr/libexec/gcc/x86_64-redhat-linux/5.2.1/ld: skipping incompatible /opt/rh/devtoolset-4/root/usr/lib/gcc/x86_64-redhat-linux/5.2.1/libstdc++.a when searching for -lstdc++
/opt/rh/devtoolset-4/root/usr/libexec/gcc/x86_64-redhat-linux/5.2.1/ld: cannot find -lstdc++
collect2: error: ld returned 1 exit status
I have tried this as well but still get the exact same error above:
g++ -static -m32 -L/opt/rh/devtoolset-4/root/usr/lib/gcc/x86_64-redhat-linux/5.2.1/32 Hello.cpp
I have tried in both orders - nothing helps.
Why is it still looking at the wrong directory?
Is using -m32 option override -L option?
I could not find much documentation on -m32 option.
Please help.
Thanks!
Why is it still looking at the wrong directory?
Compiler always looking in predefined directories first. -L options adds your path to these list of directories, so because of it compiler is stil looking at the wrong directory. For more detailed output try to compiler your program with detailed output -### or -v options.
Is using -m32 option override -L option?
The answer is no - -m32 options is option to generate 32bit code, for example:
You may generate 32bit code that will work on 32bit machine, on your 64bit machine. Also you may run this code on your 64bit machine - it will work well.
I could not find much documentation on -m32 option.
Here is the link to the GCC docs
And here is doc about directory searching options
Also to say to compiler where to find libraries, you may set
LD_LIBRARY_PATH in your env
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FULL_PATH_TO_YOUR_LIB
Do not override env vars - cause it may cause more problems if you are not absolutely sure in what you are doing.
Of late, facebook opensourced warp, C/C++ preprocessor.
https://github.com/facebook/warp
I'm trying to build it using dmd and stuck with some build errors.
I downloaded dmd.2.065.0.zip for dmd compiler - dmd2/linux/bin64/dmd
I also see a bunch of libraries, for example libphobos2.a
Then when I build warp, I see some errors from ld, that keep complaining that phobos2.a could not be found. I exported LD_LIBRARY_PATH to the dir where this library is stored but no luck.
I compiled in verbose mode, and it doesn't give more info.
Command:
/path/to//building_stuff/dmd2/linux/bin64/dmd -O -inline -release -ofwarp cmdline.d constexpr.d context.d directive.d expanded.d file.d id.d lexer.d loc.d macros.d main.d number.d outdeps.d ranges.d skip.d sources.d stringlit.d textbuf.d -v
Error excerpt:
function textbuf.Textbuf!char.Textbuf.length
function textbuf.Textbuf!char.Textbuf.resize
gcc warp.o -o warp -m64 -L/path/to/building_stuff/dmd2/linux/bin64/../lib64 -Xlinker --export-dynamic -l:libphobos2.a -lpthread -lm -lrt
/usr/bin/ld: cannot find -l:libphobos2.a
collect2: ld returned 1 exit status
--- errorlevel 1
I was hoping the D language experts here, or those who know about warp already could give me some hint.
I was not on CentOS, as warp demands. I wonder if that could anyway be the reason.
I was not using gcc 4.7.x as warp demands, but, to me, the library could just not be located doesn't look like a problem from old gcc I have.
I was on redhat5.5 machine with 4.1 gcc.
CentOS is basically a RedHat, so everything should work OK. As people commented, your real problem is the -l:libphobos2.a in your link line. Remember, GNU/Linux allows colons in file-names, so :libphobos2.a is a perfectly valid file, and GNU ld won't find it in the library search paths.
Note that they've added a make file to easy on your compilation, I managed to compile it using "make -j" and only editing the dmd command line in the make.
just rename "libphobos2.a" to "lib:libphobos2.a.a"
I faced a similar problem with ld version 2.17, but with version 2.20 this 'l:<libfilename>' kinda syntax works fine.
OS: Windows 7
I have the source, as well as all the library files I'm using in one directory, on my desktop. I'm running the shell by using msys.bat, which was created when I installed MinGW. I've tried to run the following (and many others):
g++ -I. -L. -o opengltest.exe opengltest.cpp -lglew32 -lglew32s -lglew32.dll
I recieve the following error:
c:/mingw/bin/../lib/gcc/mingw32/4.6.2/../../../../mingw32/bin/ld.exe: cannot find -lglew32.dll
collect2: ld returned 1 exit status
This also happens when I use the -L switch and the entire C:/Users/... path, but I get the same error. Again, glew32.dll is in the same directory that the .cpp is in, which is the same directory I'm working in within the shell. I've tried multiple solutions from multiple posts, and it still seems like I'm missing something. I thought using the -L. was a straightforward way to tell MinGW to look in the working directory, but apparently it doesn't work that way.
Do not link against both the dynamic and static linking version of glew in the same application. This makes no sense. Also do no link against glew32.dll, this makes equally little sense.
Most importantly, do not use the DLL version of glew with g++ at all - it will not work (see one of my previous answers to understand why). Instead, #define GLEW_STATIC (better if you use -DGLEW_STATIC as a compiler switch) and only link to glew32s.