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I am installing GSI V3.5 https://dtcenter.org/com-GSI/users/. I have no experience in gcc so I cannot use a correct terminolgy for this. After compiling the program I get an error

” ........... "/raid60/raid2/opt/local/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find Scrt1.o: No such file or directory /raid60/raid2/opt/local/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find crti.o: No such file or directory /raid60/raid2/opt/local/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lm /raid60/raid2/opt/local/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lgomp "

It seems that there is problem with gcc which cannot find the directory including Scrt1.0, crti.o and others.I found these files in this directory /home/opt/anaconda/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib. Because I do not have adminstration previlage, as suggested, I could not install packages like libc6-dev. Follwing https://askubuntu.com/questions/251978/cannot-find-crti-o-no-such-file-or-directory And https://askubuntu.com/questions/251978/cannot-find-crti-o-no-such-file-or-directory, I added the directory above to ~/.cshrc. 

 setenv LD_LIBRARY_PATH /home/opt/anaconda/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib

But still gcc does not recognize this path.

I also tried to feed this path into configure using LDFLGAS

 > ./configure > LDFLAGS="-L/home/opt/anaconda/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib"

But no success. At the end I added LDFLAGS into configure

script. But it also did not work. Any help is highly apreaciated.

Of course, the expected answer would be making gcc identify the path

of crti.o and other missing files.

UPDATE: As Florian Weimer suggested, I made the file crt.specs. I also updated related line in configure. These files are in dropbox link . But I still get the same error.

UPDATE 2. These are some lines before error occurs:

../write_obsdiags.o ../wrwrfmassa.o ../wrwrfnmma.o -L/opt/local/wrf_kpp/gsi35/comGSIv3.5_EnKFv1.1/lib -lsp_i4r8 -lsigio_i4r4 -lsfcio_i4r4 -lnemsio -lbacio -lw3nco_i4r8 -lbufr_i4r8 -lw3emc_i4r8 -lcrtm /opt/local/wrf_kpp/WRFV3//external/io_int/libwrfio_int.a /opt/local/wrf_kpp/WRFV3//external/io_netcdf/libwrfio_nf.a /opt/local/wrf_kpp/WRFV3//frame/pack_utils.o /opt/local/wrf_kpp/WRFV3//frame/module_machine.o /opt/local/wrf_kpp/WRFV3//frame/module_driver_constants.o -L/home/srvx11/lehre/users/a1276905/.conda/envs/libgsi/lib -lnetcdff -lnetcdf -L/home/srvx11/lehre/users/a1276905/.conda/envs/libgsi/lib -L/home/srvx11/lehre/users/a1276905/.conda/envs/libgsi/lib -llapack -lblas -fopenmp /raid60/raid2/opt/local/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find Scrt1.o: No such file or directory

Update 3 I have used option -B to add directory including crti.o to the search path of gcc. when I invoke 

gcc -print-search-dirs

I see my desired path "/home/opt/anaconda/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib" among known paths

libraries: =/home/opt/anaconda/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/x86_64-unknown-linux-gnu/5.3.0/:/home/opt/anaconda/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/:/usr/local/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/:/usr/local/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../../x86_64-unknown-linux-gnu/lib/x86_64-unknown-linux-gnu/5.3.0/:/usr/local/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../../x86_64-unknown-linux-gnu/lib/../lib64/:/usr/local/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../x86_64-unknown-linux-gnu/5.3.0/:/usr/local/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../../lib64/:/lib/x86_64-unknown-linux-gnu/5.3.0/:/lib/../lib64/:/usr/lib/x86_64-unknown-linux-gnu/5.3.0/:/usr/lib/../lib64/:/usr/local/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../../x86_64-unknown-linux-gnu/lib/:/usr/local/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/../../../:/lib/:/usr/lib/

But I am not through.

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The linker search path is only used for libraries. It is not used to locate any object files, including the startup object files.

If the toolchain was built with sysroot support, you can use --sysroot to change where GCC looks for most of its files. This may require adding symbolic links or copying files to create a working sysroot environment and can be somewhat cumbersome.

If you want to change just the location of the startup files, you can do so with a custom GCC specs file. What you need to use is unfortunately somewhat dependent on the GCC version and how GCC was built. This means that as a starting point, you need to use the specs built into GCC, which you can obtain using this command:

gcc -dumpspecs

There are two sections in this file, *startfile: and *endfile:, that are of interest. Copy those two lines and the line following each into a new file, say crt.specs. Edit them and replace Scrt1.o, crt1.o, crti.o (in *startfiles:) and crtn.o (in *endfiles:) with the absolute path to the files you want to use (presumable files you have extracted from libc6-dev using dpkg -x).

Then you can use the new specs by invoking GCC using:

gcc --specs=crt.specs

It will definitely save you a lot of trouble if you can get the system administrator to install the libc6-dev package. It is the only safe way to ensure that these files are kept up-to-date along with the libc6 package.

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6 Comments

Dear @Florian Weimer, Thanks for your reply. I have implemented your suggestion. But I got the same error. I will add created files (crt.specs) and configure in the update of the my question.
Have you verified the specs file is actually used? LDFLAGS doesn't show specs=/path/to/crt.specs, so that might be the reason why it doesn't work.
I have two lines in configure which I think should be updated: DM_CC = gcc --specs=/opt/local/wrf_kpp/gsi35/comGSIv3.5_EnKFv1.1/crt.specs and SCC = gcc --specs=/opt/local/wrf_kpp/gsi35/comGSIv3.5_EnKFv1.1/crt.specs.
Hmm. Please add the actual linker command leading to the error to the question.
Sorry I know it is annoying to you. But I do not know what you mean with acutal linker command. I have one configure and one compile file. Do you want me to publish the content of these files?
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