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scottransom / presto

Open source pulsar search and analysis toolkit
http://www.cv.nrao.edu/~sransom/presto/
GNU General Public License v2.0
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compiling current master gives error: undefined reference to `read_wisdom' #68

Open gijzelaerr opened 8 years ago

gijzelaerr commented 8 years ago 
search_bin.o: In function `main':
/packaging/repos/presto/src/search_bin.c:206: undefined reference to `read_wisdom'
gcc -I/packaging/repos/presto/include -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -I  -DUSEFFTW -DUSEMMAP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wall -W -fPIC -O3 -ffast-math -Wno-unused-result -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -fopenmp -o /packaging/repos/presto/bin/prepsubband prepsubband.o prepsubband_cmd.o backend_common.o zerodm.o sigproc_fb.o psrfits.o -lcfitsio -lpthread -L/packaging/repos/presto/lib -lpresto -lfftw3f -lcfitsio -lm
collect2: error: ld returned 1 exit status
Makefile:296: recipe for target 'search_bin' failed

looks like read_wisdom is defined in include/ransomfft.h, but when I include that it fails even more. removing read_wisdom seems to solve the problem, not sure if that is the smartest thing to do.

scienceguyrob commented 7 years ago

Hi Scott, I'm having the same issue. I'm running CentOS 7. I'm building within a Docker container, so I can offer the exact environment required to reproduce this issue. My docker file is on Github:

https://raw.githubusercontent.com/scienceguyrob/Docker/master/Images/tvg/CentOS/Dockerfile (commit 58a0dcf). Not sure if this helps!

siemion commented 6 years ago

I had this problem as well under Ubuntu 16.04 LTS (gcc 5.4.0)

Fixed by changing gcc flag ordering in the Makefile:

CFLAGS = -I$(PRESTO)/include $(GLIBINC) $(CFITSIOINC) $(PGPLOTINC) $(FFTINC) \
    -g -Wall -W -fPIC -O3 -ffast-math -DUSEFFTW -DUSEMMAP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
scottransom commented 6 years ago

Huh. I've never been able to replicate this bug. And I use Ubuntu 14.04, 16.04 and now 18.04. @siemion Any idea why that change in the CFLAGS ordering makes a difference?

siemion commented 6 years ago

No idea... =)

Here's the full compiler info:

gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/5/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.9' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.9)
oleas-juan commented 5 years ago

Hi @scottransom,

I've tried installing Presto in a Redhat 6.10 OS machine, in a CentOS 7 machine, and a Ubuntu 18.04 machine and they all give me this bug.

I tried fixing it by following @siemion suggestion of editing the gcc flag ordering in the Makefile, but I still get the error.

Since you've never been able to replicate this bug, what were your configurations/ did you try to compile presto on a new machine that is fresh out of the box? If so, what dependencies did you install that are not listed on the INSTALL file.

Thanks

oleas-juan commented 5 years ago

Here is my compiler info on my Ubuntu 18.04 machine:

gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.4.0-1ubuntu1~18.04.1' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix gcc version 7.4.0 (Ubuntu 7.4.0-1ubuntu1~18.04.1)

scottransom commented 5 years ago

Ugh. This is so strange. I regularly compile PRESTO on RHEL7, RHEL6, and all the recent Ubuntu releases (I'm using 18.10 on my laptop now, and will probably try 19.04 this weekend). And yes, I compile PRESTO in out-of-the box configurations of those quite regularly.

Are you compiling your own FFTW? Or are you using a package for it?

And what if you remove search_bin from the BINARIES target? Does everything else compile?

scottransom commented 5 years ago

Did you by any chance get rid of the -DUSEFFTW flag in CFLAGS? That would cause this as well, I think.

oleas-juan commented 5 years ago

Yeah, it's a strange one. On the Ubuntu machine, I'm using the libfftw3-dev package that was suggested. On the others, I was compiling my own FFTW.

I haven't tried removing the search_bin from the BINARIES. By this, do you mean removing search_bin.c, search_bin_cmd.c, search_bin_cmd.o, and search_bin.o from the $PRESTO/src directory?

I just tried now with removing the -DUSEFFTW flag in CFLAGS and it still didn't work.

scottransom commented 5 years ago

If you look in $PRESTO/src/Makefile, search_bin is listed in the BINARIES variable. Just remove the word from there and search_bin won't be compiled by default. I want to see if everything else compiles and runs fine. (i.e. is this a problem just with search_bin, or with other parts of PRESTO that use FFTW).

As for -DUSEFFTW, I was wondering if that was not being set somehow. If that is not set, I can completely see how this error would happen. In other words, you should definitely have that as part of CFLAGS.

oleas-juan commented 5 years ago

Follow up: I removed search_bin from the BINARIES variable, and proceeded to compile it and I got this new error now:

accel_utils.o: In functioninit_subharminfo': accel_utils.c:(.text+0xa95): undefined reference to fftwcall' accel_utils.o: In functionsubharm_fderivs_vol': accel_utils.c:(.text+0x6361): undefined reference to fftwcall' collect2: error: ld returned 1 exit status Makefile:206: recipe for target 'accelsearch' failed make: *** [accelsearch] Error 1

Should I remove accelsearch from the BINARIES?

scottransom commented 5 years ago

Ok, that is useful. This definitely means that, for some reason, USEFFTW is not being set properly.

Can you please post what one of the gcc lines looks like when you run "make" in $PRESTO/src?

And no, you definitely want to keep accelsearch in BINARIES

oleas-juan commented 5 years ago

This is one of the gcc lines when running "make" in $PRESTO/src:

gcc -I/home/oleasjuan/software/presto/include -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I -g -Wall -W -fPIC -O3 -ffast-math -DUSEFFTW -DUSEMMAP -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -Wno-unused-result -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -fopenmp -o /home/oleasjuan/software/presto/bin/makedata com.o randlib.o makedata.o -lcfitsio -lpthread -L/home/oleasjuan/software/presto/lib -lpresto -lfftw3f -lm

scottransom commented 5 years ago

That last "empty" -I might be the problem. It seems like the FFTW include location isn't being found. What do you get if you run pkg-config --cflags fftw3f on the command line? (Note that that is in the Makefile to find the FFTW include files).

If that doesn't give you an include path, you might need to set FFTINC explicitly to the include directory where fftw3.h lives.

oleas-juan commented 5 years ago

Hi, so I ran the command pkg-config --cflags fftw3f and I got this -I/usr/local/include

Would I still need to set FFTINC explicitly o include the directory where ffw3.h lives? Is so, would I set this on my .bashrc file?

oleas-juan commented 5 years ago

Follow up, I uninstalled and manually reinstalled FFTW3, Tempo, cfitsio, and pgplot, and edited my .bashrc file to this:

export PATH="/home/oleasjuan/anaconda3/bin:/home/oleasjuan/software/presto/bin:$
PATH"
export PYTHONPATH="/home/oleasjuan/anaconda3/bin:/home/oleasjuan/software/presto
/lib/python"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/oleasjuan/software/presto/lib"
export PRESTO="/home/oleasjuan/software/presto"
export PGPLOT_DIR="/usr/local/pgplot"
export PGPLOT_DEV="/XServe"
export TEMPO="/home/oleasjuan/software/tempo"
export CFITSIO_DIR="/home/oleasjuan/software/cfitsio-3.47"
export FFTW3F_DIR="/home/oleasjuan/software/fftw-3.3.8"

export PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/local/include:/home/oleasjuan/soft
ware/fftw-3.3.8:/usr/share/glib-2.0:/home/oleasjuan/software/cfitsio-3.47:/home/
oleasjuan/software/presto/include"

This seems to not give issues with FFTW. However, I get this new error when trying to compile it:

/usr/bin/ld: warning: libcurl.so.4, needed by /home/oleasjuan/software/cfitsio-3.47/lib/libcfitsio.so, not found (try using -rpath or -rpath-link)
/home/oleasjuan/software/cfitsio-3.47/lib/libcfitsio.so: undefined reference to `curl_easy_setopt'
/home/oleasjuan/software/cfitsio-3.47/lib/libcfitsio.so: undefined reference to `curl_global_cleanup'
/home/oleasjuan/software/cfitsio-3.47/lib/libcfitsio.so: undefined reference to `curl_easy_init'
/home/oleasjuan/software/cfitsio-3.47/lib/libcfitsio.so: undefined reference to `curl_easy_perform'
/home/oleasjuan/software/cfitsio-3.47/lib/libcfitsio.so: undefined reference to `curl_easy_cleanup'
/home/oleasjuan/software/cfitsio-3.47/lib/libcfitsio.so: undefined reference to `curl_global_init'
collect2: error: ld returned 1 exit status
Makefile:234: recipe for target 'prepdata' failed
make: *** [prepdata] Error 1
scottransom commented 5 years ago

Given what you got with the pkg-config command, I think that that "empty" -I should have been -I/usr/local/include. You could try manually setting that in the makefile for FFTINC.

The libcurl issue isn't a PRESTO problem, though, but is related to the installation of CFITSIO. You could try a "locate libcurl.so.4" to see if that exists on your system. But curl is definitely a package in all of the Linuxes.

vtonder commented 3 years ago

Hi Scott,

I'm on Ubuntu 20.04 and I got the same issue as described above - changing the gcc flag ordering as per Andrew's suggestion also fixed it for me.

Thanks,

scottransom commented 3 years ago

@vtonder Thanks for that. I've changed the ordering in the official PRESTO even though I have no idea why that works. Seems really bizarre to me....