How to make gdb to use different directory to look for source files.
For example my source file during the compilation was in directory:
/home/foo/bar.c
Next, I moved it into directory:
/tmp/debug/home/foo/bar.c
How to enforce gdb to search in this directory?
According to this site I should just use command:
dir /tmp/debug/
But it is not working. I get a message foo.c: "No such file or directory" from gdb.
set substitute-path /home/foo /tmp/debug/home/foo
http://sourceware.org/gdb/current/onlinedocs/gdb/Source-Path.html#index-set-substitute_002dpath
Related
I have Icarus Verilog installed on macos, but when I run it in the terminal to get a .vcd file, it always give me these messages:
ben#Bens-macbook ~ % iverilog -o khanh.vvp khanh_tb.v
khanh_tb.v: No such file or directory
No top level modules, and no -s option.
Can anyone help me with this problem?
Those error messages mean that the input file (khanh_tb.v) is not in your current directory.
Either change your current directory to the one where the file is, or run iverilog and specify the path to the .v file:
iverilog -o khanh.vvp path/to/khanh_tb.v
path/to/ is just an example; you should change it to the directory where the file resides.
I just installed CD-HIT and followed these instructions:
Installation
Most CD-HIT programs were written in C++. Installing CD-HIT package is very simple:
download current CD-HIT at http://bioinformatics.org/cd-hit, for example cd-hit-2006-0215.tar.gz
unpack the file with ” tar xvf cd-hit-2006-0215.tar.gz --gunzip”
change dir by “cd cd-hit-2006”
compile the programs by “make”
you will have all cd-hit programs compiled
I followed these steps and indeed .exe files were made:
cdhit.c++ cdhit-est-2d.c++ clstr_select_rep.pl
cd-hit.exe cd-hit-est-2d.exe clstr_size_histogram.pl
cdhit.o cdhit-est-2d.o clstr_size_stat.pl
cdhit-2d.c++ cd-hit-para.pl clstr_sort_by.pl
cd-hit-2d.exe cdhit-utility.c++ clstr_sort_prot_by.pl
cdhit-2d.o cdhit-utility.h clstr_sql_tbl.pl
cd-hit-2d-para.pl cdhit-utility.o clstr_sql_tbl_sort.pl
cdhit-454.c++ ChangeLog clstr2tree.pl
cd-hit-454.exe clstr_cut.pl clstr2txt.pl
cdhit-454.o clstr_list.pl clstr2xml.pl
cd-hit-auxtools clstr_list_sort.pl doc
cdhit-common.c++ clstr_merge.pl FET.pl
cdhit-common.h clstr_merge_noorder.pl license.txt
cdhit-common.o clstr_quality_eval.pl make_multi_seq.pl
cdhit-div.c++ clstr_quality_eval_by_link.pl Makefile
cd-hit-div.exe clstr_reduce.pl plot_2d.pl
cdhit-div.o clstr_renumber.pl plot_len1.pl
cd-hit-div.pl clstr_rep.pl psi-cd-hit
cdhit-est.c++ clstr_reps_faa_rev.pl README
cd-hit-est.exe clstr_rev.pl usecases
cdhit-est.o clstr_select.pl
However when I typ: cd-hit-est in the cygwin command line, it will say: -bash: cd-hit.exe: command not found. I'm not able to figure out why this is happening. Even when I'm in the folder were the .exe files are located it still will give the same error.
When you try to run command without a path, bash tries to find the command name in each directory from the PATH environment variable.
Usually current directory "." is not in the PATH so you have to run command adding absolute or relative path before command name:
./cd-hit.exe
or
/absolute/path/to/your/cd-hit/program/cd-hit.exe
If you want to permanently run command cd-hit.exe from anywhere, just add the directory where cd-hit was compiled to any existing auto-loaded bash profile files:
.profile
.bashrc
.bash_profile
like
PATH=$PATH:/absolute/path/to/your/cd-hit/program
export PATH
I have installed the cds library with command ./build.sh -b 64 -z '-std=c++0x' -l '-L /usr/lib/x86_64-linux-gnu' --with-boost /usr/include/boost --amd64-use-128bit at build folder.
After I tried to compile the example init.cpp of src folder, I typed this in terminal: g++ init.cpp -o init, and terminal showed: fatal error: cds/init.h: No such file or directory.
What should I do for compilation command in this case?
Thanks.
For general troubleshooting in cases like this, i would recommend finding where on the system the file got installed (if your build.sh actually installed the file). You would be able to find the missing header file using
find / -path '*/cds/init.h' 2>/dev/null
Then you need to supply two parameters to g++:
First one gets the compiler to know about the include files from the install directory
-I path_to_folder_one_step_above_cds_folder
Second one gets the linker to know about the librarys location. If the library file is called libcds.so, you can find it by running
find / -name libcds.so 2>/dev/null
So for linking, you supply the flag
-L path_to_folder_one_step_above_libcds.so
In your case you might not need the -L flag, since most of your library supposedly is header only.
UPDATE: the build.sh script is printing out important information at the top, starting with "Building with the following options:". The important bits will be "Compile options:" and "Link options:". Those should be enough to solve your specific option.
UPDATE2: build.sh also exports some flags which might include more options. You can print them out directly after running build.sh by running
echo LDFLAGS=$LDFLAGS
echo CFLAGS=$CFLAGS
echo CXXFLAGS=$CXXFLAGS
you are likely to need to pass all these options to g++ when compiling and linking against that library. LDFLAGS are specific to the linker only. Both the other ones are needed for compiling c++ files.
I'm a bit of a noob at working with compilers. I want to add an arbitrary directory on my win 8 C:\ drive to the Cygwin gcc default search path.
Here is what I have tried so far. Using gcc --help I found the commands -print-search-dirs and -B <directory> ("add directory to the compiler's search path").
Using the former command output this:
install: /usr/lib/gcc/x86_64-pc-cygwin/4.9.2/
programs: =/usr/lib/gcc/x86_64-pc-cygwin/4.9.2/:/usr/lib/gcc/x86_64-pc-cygwin/4.
9.2/:/usr/lib/gcc/x86_64-pc-cygwin/:/usr/lib/gcc/x86_64-pc-cygwin/4.9.2/:/usr/li
b/gcc/x86_64-pc-cygwin/:/usr/lib/gcc/x86_64-pc-cygwin/4.9.2/../../../../x86_64-p
c-cygwin/bin/x86_64-pc-cygwin/4.9.2/:/usr/lib/gcc/x86_64-pc-cygwin/4.9.2/../../.
./../x86_64-pc-cygwin/bin/
libraries: =/usr/lib/gcc/x86_64-pc-cygwin/4.9.2/:/usr/lib/gcc/x86_64-pc-cygwin/4
.9.2/../../../../x86_64-pc-cygwin/lib/x86_64-pc-cygwin/4.9.2/:/usr/lib/gcc/x86_6
4-pc-cygwin/4.9.2/../../../../x86_64-pc-cygwin/lib/../lib/:/usr/lib/gcc/x86_64-p
c-cygwin/4.9.2/../../../x86_64-pc-cygwin/4.9.2/:/usr/lib/gcc/x86_64-pc-cygwin/4.
9.2/../../../../lib/:/lib/x86_64-pc-cygwin/4.9.2/:/lib/../lib/:/usr/lib/x86_64-p
c-cygwin/4.9.2/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-pc-cygwin/4.9.2/../../../..
/x86_64-pc-cygwin/lib/:/usr/lib/gcc/x86_64-pc-cygwin/4.9.2/../../../:/lib/:/usr/
lib/
The full path to /usr is C:\cygwin64\usr. The directory I want to add is c:\directory So I tried gcc -B /../directory and other variations, but I get error
gcc: fatal error: no input files
compilation terminated
Seems like it thinks I'm trying to compile something. I want to permanently add a directory to the list of default search paths.
There are two issues at play here.
The first problem has to do with the fact that Cygwin views the top of its directory tree / to be within the Windows directory C:\cygwin64. As a result, you are unable to move above that point in the filesystem. The solution is to go through Cygwin's directory /cygdrive, which is the access point where all Windows disk drives are mounted. You can access the top-level Windows directory C:\ from Cygwin as /cygdrive/c. So for the problem above, instead of using gcc -B /../directory, try using gcc -B /cygdrive/c/directory.
The second issue is that of adding directories to the search path, versus telling it to compile a specific source file. Given the date of this question, I assume you've solved that part of the problem at this point?
Sometimes I forget I'm in the build folder and I run the command in the root directory. Well, maybe some of you have experienced that this creates a mess in the entire file hierarchy, as you have to delete CMakeFiles/ folder, config files, and files related to CPack and CTest. Is there a way I can add something to the Makefile at the root directory that prevents me from running cmake accidentally? I tried to add a target 'cmake' but this didn't work.
aa
UPDATE
I found the same question posted in here. I ended up adopting to put a function in my .bashrc file as suggested in that page:
function cmake() {
# Don't invoke cmake from the top-of-tree
if [ -e "CMakeLists.txt" ]
then
echo "CMakeLists.txt file present, cowardly refusing to invoke cmake..."
else
/usr/bin/cmake $*
fi
}
You can check in your CMakeLists.txt if the source and binary directories are the same. Put something like this as the very first thing in your CMakeLists.txt:
if (CMAKE_BINARY_DIR STREQUAL CMAKE_SOURCE_DIR)
message(FATAL_ERROR "Source and build directories cannot be the same.")
endif()