relocation truncated to fit: R_X86_64_PC32 error

[Anonymous]

Discussion moved from here

Dear Prof. Meyer,
Thanks for your quick reply!
I have tried what you suggested, but it still did not work.
By the way, when I run the following code :(according to the post Calculating reaction rates)
cd nucnet-tools-code/build
make clean_all
make -f Makefile.libnucnet all_libnucnet
I got a similar error saying:
/tmp/ccArEZHJ.o：In function ‘main’：
/home/David/nucnet-tools-code/build/../vendor/libnucnet/0.35/src/../examples/average_zones.c:152：undefined reference to ‘gsl_vector_scale’
/home/David/nucnet-tools-code/build/../vendor/libnucnet/0.35/src/../examples/average_zones.c:152:(.text+0x3ac): relocation truncated to fit: R_X86_64_PC32 against undefined symbol gsl_vector_scale
/home/David/nucnet-tools-code/build/../vendor/libnucnet/0.35/src/../examples/average_zones.c:154：undefined reference to ‘gsl_vector_add’
/home/David/nucnet-tools-code/build/../vendor/libnucnet/0.35/src/../examples/average_zones.c:154:(.text+0x3c2): relocation truncated to fit: R_X86_64_PC32 against undefined symbol gsl_vector_add
/home/David/nucnet-tools-code/build/../vendor/libnucnet/0.35/src/../examples/average_zones.c:166：undefined reference to ‘gsl_vector_scale’
/home/David/nucnet-tools-code/build/../vendor/libnucnet/0.35/src/../examples/average_zones.c:166:(.text+0x408): relocation truncated to fit: R_X86_64_PC32 against undefined symbol gsl_vector_scale
collect2: error: ld returned 1 exit status
make: *** [Makefile.libnucnet:84: average_zones] Error 1"
I am not sure if these two problems might have a same origin.
Best wishes.

[Bradley S. Meyer]

Thanks for this post. The problem you encountered is more subtle than I first realized. I wonder if you can reply and tell me the kind of computer and operating system you have. In the meantime, I'll read on this issue. Best wishes.

[Anonymous]

Dear Prof. Meyer,

Thanks for your reply.
My computer is Lenovo Thinkpad X280 based on x64 CPU with 64-bit Windows 10 operating system.

Best wishes.

[Bradley S. Meyer]

Thanks. Are you running cygwin? Also, what is the result of

gsl-config --version

Best wishes.

[Anonymous]

Dear Prof. Meyer,

Yes, I am running cygwin. And the version of gsl is 2.3.
Thanks for your attention!

Best wishes.

[Bradley S. Meyer]

Let's make sure the attached simple program test.c works. Try typing:

gcc `gsl-config --cflags --libs` test.c 
./a.out

I get

v_0 = 1.845
v_1 = 3.345
v_2 = 4.845

[Anonymous]

Dear Prof. Meyer,

After typting : gcc gsl-config --cflags --libs test.c
it prints out:

/tmp/ccynXjMh.o:test.c:(.text+0x13)：undefined reference to ‘gsl_vector_alloc’
/tmp/ccynXjMh.o:test.c:(.text+0x13): relocation truncated to fit: R_X86_64_PC32 against undefined symbol gsl_vector_alloc
/tmp/ccynXjMh.o:test.c:(.text+0x21)：undefined reference to ‘gsl_vector_alloc’
/tmp/ccynXjMh.o:test.c:(.text+0x21): relocation truncated to fit: R_X86_64_PC32 against undefined symbol gsl_vector_alloc
/tmp/ccynXjMh.o:test.c:(.text+0x49)：undefined reference to ‘gsl_vector_set’
/tmp/ccynXjMh.o:test.c:(.text+0x49): relocation truncated to fit: R_X86_64_PC32 against undefined symbol gsl_vector_set
/tmp/ccynXjMh.o:test.c:(.text+0x67)：undefined reference to ‘gsl_vector_set’
/tmp/ccynXjMh.o:test.c:(.text+0x67): relocation truncated to fit: R_X86_64_PC32 against undefined symbol gsl_vector_set
/tmp/ccynXjMh.o:test.c:(.text+0x81)：undefined reference to ‘gsl_vector_add’
/tmp/ccynXjMh.o:test.c:(.text+0x81): relocation truncated to fit: R_X86_64_PC32 against undefined symbol gsl_vector_add
/tmp/ccynXjMh.o:test.c:(.text+0x99)：undefined reference to ‘gsl_vector_scale’
/tmp/ccynXjMh.o:test.c:(.text+0x99): relocation truncated to fit: R_X86_64_PC32 against undefined symbol gsl_vector_scale
/tmp/ccynXjMh.o:test.c:(.text+0xb4)：undefined reference to ‘gsl_vector_get’
/tmp/ccynXjMh.o:test.c:(.text+0xb4): relocation truncated to fit: R_X86_64_PC32 against undefined symbol gsl_vector_get
/tmp/ccynXjMh.o:test.c:(.text+0xfe)：undefined reference to ‘gsl_vector_free’
/tmp/ccynXjMh.o:test.c:(.text+0xfe): relocation truncated to fit: R_X86_64_PC32 against undefined symbol gsl_vector_free

It seems there are some problems to link to GSL library, I found a post in which such a problem is discussed and another command is used to run the test file.

So I tried typing:

gcc test.c $(gsl-config --cflags --libs)
./a.exe

I can get the same result with yours:
v_0 = 1.845
v_1 = 3.345
v_2 = 4.845

But I don't know what is the key point of such difference.

Thank you.
Best wishes.

[Bradley S. Meyer]

Interesting. You might change the

CINCLUDE += `xml2-config --cflags` \
            `gsl-config --cflags`  \
            -I$(LIBNUCNETDIR)      \
            -I$(WNMATRIXDIR)       \
            -I$(LIBSTATMECHDIR)    \
            -I$(LIBNUCEQDIR)       \
            -I$(NUCNET_TARGET)     \

in the build/Makefile to

CINCLUDE += $(xml2-config --cflags) \
            $(gsl-config --cflags)  \
            -I$(LIBNUCNETDIR)      \
            -I$(WNMATRIXDIR)       \
            -I$(LIBSTATMECHDIR)    \
            -I$(LIBNUCEQDIR)       \
            -I$(NUCNET_TARGET)     \

And

  CLIBS += `xml2-config --libs` `gsl-config --libs`

to

  CLIBS += $(xml2-config --libs) $(gsl-config --libs)

and see what happens when you recompile. Let me know. Best wishes.

[Anonymous]

Dear Prof. Meyer,

I type make -f Makefile.libnuceq clean
make -f Makefile.libnuceq alllibnuceq
It shows:

In file included from ../vendor/wn_matrix/0.19/src/WnMatrix.c:40:0:
../vendor/wn_matrix/0.19/src/WnMatrix.h:49:10: fatal error：libxml/hash.h：No such file or directory

[Bradley S. Meyer]

Do you have libxml2 installed? For example, what happens if you type

xml2-config --version

Best wishes.

[Anonymous]

Dear Prof. Meyer,

I have installed libxml2, the result of xml2-config --version is 2.9.9

Best wishes.

[Bradley S. Meyer]

Thanks. I think the issue is that the Makefile is not executing the xml2-config and gsl-config commands. Let's try what we did above but indicate the shell command:

CINCLUDE += `xml2-config --cflags` \
            `gsl-config --cflags`  \
            -I$(LIBNUCNETDIR)      \
            -I$(WNMATRIXDIR)       \
            -I$(LIBSTATMECHDIR)    \
            -I$(LIBNUCEQDIR)       \
            -I$(NUCNET_TARGET)     \

in the build/Makefile to

CINCLUDE += $(shell xml2-config --cflags) \
            $(shell gsl-config --cflags)  \
            -I$(LIBNUCNETDIR)      \
            -I$(WNMATRIXDIR)       \
            -I$(LIBSTATMECHDIR)    \
            -I$(LIBNUCEQDIR)       \
            -I$(NUCNET_TARGET)     \

And

  CLIBS += `xml2-config --libs` `gsl-config --libs`

to

  CLIBS += $(shell xml2-config --libs) $(shell gsl-config --libs)

Note the addition of shell to what I suggested before. Then try recompiling. Let me know what happens. Best wishes.

[Anonymous]

Dear Prof. Meyer,

I modified Makefile and then type:
make -f Makefile.libnuceq cleanall_libnuceq
make -f Makefile.libnuceq all_libnuceq

It returns the same error as the very beginning, just like:
/home/David/nucnet-tools-code/build/../vendor/libnuceq/0.7/src/../examples/compute_function_integrand_wse.c:376：undefined reference to ‘gsl_sf_fermi_dirac_half’
/home/David/nucnet-tools-code/build/../vendor/libnuceq/0.7/src/../examples/compute_function_integrand_wse.c:376：(.text+0x981): relocation truncated to fit: R_X86_64_PC32 against undefined symbol 'gsl_sf_fermi_dirac_half'

Best wishes.

[Bradley S. Meyer]

This seems like it is getting very specific to your system. Could I ask you to contact me directly at mbradle at clemson dot edu? Thanks, and best wishes.

[Anonymous]

Dear Prof. Meyer,
I am new here. I want to compute nuclear statistical equilibrium. I have downleded the C codes. Now i want to know how to use these codes? Is it necessary to have a linux system for it? Can i use C++ software for it?

[Bradley S. Meyer]

I moved this discussion here.