I am using amber12 software used for molecular mechanical force fields for the simulation of biomolecules, I follow the installation instructions described in the next link Intallation of amber in Mac OS X the program actually works but when in try to execute a program part of the software its stops and says
Fortran runtime error: End of file
1.So this is what I do, first access the file folder that contain the files
N-terminal-2:~ javieralejandrorendoncarrillo$ cd Desktop/amber/Complex1
2.then set the path
N-terminal-2:Complex1 javieralejandrorendoncarrillo$ export AMBERHOME=/Users/javieralejandrorendoncarrillo/amber/amber12
3.and finally execute the program whit the next command line:
N-terminal-2:Complex1 javieralejandrorendoncarrillo$ $AMBERHOME/bin/sander.MPI -O -i min.in -o min_complex.out -p complex.prmtop -c complex.inpcrd -r complex_min.crd &
[2] 13377
N-terminal-2:Complex1 javieralejandrorendoncarrillo$ At line 524 of file mdread.F90 (unit = 5, file = 'min.in')
Fortran runtime error: End of file
[2]- Exit 2 $AMBERHOME/bin/sander.MPI -O -i min.in -o min_complex.out -p complex.prmtop -c complex.inpcrd -r complex_min.crd
N-terminal-2:Complex1 javieralejandrorendoncarrillo$
The file min.in is saved in file folder Complex 1 where I'm running the simulation this is the script for min.in
Initial minimisation of our complex
&cntrl
imin=1, maxcyc=3000, ncyc=2500,
cut=16, ntb=0, igb=1,
&end
How do I solve this problem? Is the syntax wrong? Does anyone know how to execute or what kind of programming language is this?
This is the version installed of gfortran I have
N-terminal-2:~ javieralejandrorendoncarrillo$ gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/opt/local/libexec/gcc/x86_64-apple-darwin12/4.7.2/lto-wrapper
Target: x86_64-apple-darwin12
Configured with: ../gcc-4.7.2/configure --prefix=/opt/local --build=x86_64-apple-darwin12 --enable-languages=c,c++,objc,obj-c++,lto,fortran,java --libdir=/opt/local/lib/gcc47 --includedir=/opt/local/include/gcc47 --infodir=/opt/local/share/info --mandir=/opt/local/share/man --datarootdir=/opt/local/share/gcc-4.7 --with-libiconv-prefix=/opt/local --with-local-prefix=/opt/local --with-system-zlib --disable-nls --program-suffix=-mp-4.7 --with-gxx-include-dir=/opt/local/include/gcc47/c++/ --with-gmp=/opt/local --with-mpfr=/opt/local --with-mpc=/opt/local --with-ppl=/opt/local --with-cloog=/opt/local --enable-cloog-backend=isl --disable-cloog-version-check --enable-stage1-checking --disable-multilib --enable-lto --enable-libstdcxx-time --with-as=/opt/local/bin/as --with-ld=/opt/local/bin/ld --with-ar=/opt/local/bin/ar --with-bugurl=https://trac.macports.org/newticket --disable-ppl-version-check --with-pkgversion='MacPorts gcc47 4.7.2_2'
Thread model: posix
gcc version 4.7.2 (MacPorts gcc47 4.7.2_2)
I had the same error message: ..file mdread.F90 (unit = 5, file = 'min_all.in')...
When investigating this, I for some reason found that changing the ntpr=5 to 6 in the min_all.in file got rid of the problem:
&cntrl
imin=1, maxcyc=200,
ntpr=6,
&end
Not being the sharpest knife in the drawer about these things, I have a hard time seeing why this solved it for me though.
The ntpr value only defines how often the trajectory coordinates should be sent to the out-file, in this case every 6 steps instead of every 5 steps.
Extended comment rather than an answer. The two common causes of the error message you are getting, that is
At line 524 of file mdread.F90 (unit = 5, file = 'min.in') Fortran runtime error: End of file
are
The file being read is not where the program is looking for it.
The program tries to read more data out of the file than the file contains.
From what you have posted it seems that (1) is unlikely, but you could check this by inserting an INQUIRE statement to check the file's existence prior to opening it. Alternatively you could make use of the STATUS='old' keyword (and value) in your file OPEN statement, if the file does not exist the program will report an error.
As for (2), you're pretty much on your own. No-one here (unless you are very very lucky) is likely to have a clue what your program expects to read from the input file, and you don't post any of the relevant code. You might care to modify the file READ statements to incorporate an END= keyword argument to smoke out the source of the error.
I presume that the suppliers of Amber12 are themselves likely to be more knowledgeable about their code than the SO community; your question would be better directed to them.
For what it's worth I think that the problem is unrelated to the compiler you are using.
The '&end' or '/' line should not be the last line in your input script. Have a new empty line after the '&end' or '\' line, whichever you are using.
This fixed the problem for me.
Related
I build the LLVM from source in release edtion.Now get the loop or cycle information is what i need.But it just can't work.
$opt -passes=print<cycles> input.ll -o /dev/null
zsh: no such file or directory: cycles
The unix command opt -passes=print<cycles> input.ll means to run the command opt -passes=print while reading from the file named cycles and writing to the file named input.ll.
Have a look at the answers to this question for more about this shell syntax.
You may want to use opt -passes='print<cycles>', that will at least not be interpreted by the shell, but I fear that won't work either. I've no idea what print<cycles> is supposed to achieve.
I just switched to ubuntu and I wanted to setup notepad++ for CPP.
So I used the NppExec plugin to compile within notepad++,
My script was :
npp_save
g++ "$(FULL_CURRENT_PATH)" -o "$(CURRENT_DIRECTORY)\$(NAME_PART)obj"
./"$(NAME_PART)obj"
Here the "obj" I used is to just save the file with an "obj" keyword nothing else.
The last line ./"$(NAME_PART)obj" is to run the program.
But it looks not working in ubuntu, it produces this error:
NPP_SAVE: Z:\home\username\cpp\test.cpp
g++ "Z:\home\username\cpp\test.cpp" -o "Z:\home\username\cpp\testobj"
; about to start a child process: "g++ "Z:\home\username\cpp\test.cpp" -o "Z:\home\username\cpp\testobj"
CreatProcess() failed with error code 2:
File not found.
./"testobj"
; about to start a child process: "./"testobj""
CreatProcess() failed with error code 2:
File not found.
I have investigated some of what I think is the problem, so I think is the usage of / and \ in changing the directory.
I don't know how to fix that, so I can not be sure.
Any ideas? :) I am using vim btw in the same machine and it is working perfectly.
In theory it might be possible (see below), in practice it is rather convoluted and works only for simple compiles (like single file hello world type).
I would suggest you try a linux program, e.g.
an editor like
scite (same editing engine as notepad++) or
kate
or a real IDE like
kdeveloper or
qtcreator.
The problems with Notepad++ inside wine and g++ outside wine (from the linux install ) are this:
notepad++ inside wine under linux is still a windows program
NppExec can only do, what a cmd inside wine can do.
starting g++ directly inside cmd is an error due to g++ being a linux binary and not a windows binary
that is your CreatProcess() failed with error code 2, it means: you are trying to execute a linux program inside wine.
That does not work! (At least not so easy.)
Though you can start linux program inside cmd inside wine using start /unix ...
started this way, g++ wants linux paths and NppExec through its variables will provide only windows paths (whatever wine has set up as drives like Z:\home\username\src\hello.cpp)
though you can convert wine paths to linux paths via the winepath -u command.
g++ started through 'start /unix ... ' inside a cmd inside wine has no proper terminal to report errors to you
though you can start an xterm for g++ and have g++ reports its messages to the xterm
the downside is that g++ will report errors using the linux paths in the xterm, so you cannot double click on an error message an get to the corresponding filename and line.
You get the idea: its complicated not comfortable.
What worked for me for a helloword.cpp was this NppExec script:
NPP_SAVE
npp_run cmd /c start /unix /usr/bin/xterm -e "/usr/bin/winepath -u '$(FULL_CURRENT_PATH)' | xargs g++ -o /tmp/a.out && /tmp/a.out ; echo 'Press return'; read"
The second line
uses an xterm,
let winepath convert the Z:\home\... path to /home/... and
have that send to g++ for compilation using /tmp/a.out as binary
if compile is successfull, /tmp/a.out is executed
the echo and read are for keeping the xterm open so that you can read the output.
If you really want to use Notepad++ inside wine, one option might be using Gnu Make outside of wine and have NppExec run make all or make run similar to the g++ in my script example. That would work for more complicated compiles.
I have found several conflicting answers over this topic. This blog post requires libuwind, but that doesn't work on Mac OS X. I included #include <google/profiler.h> in my code, however my compiler (g++) could not find the library. I installed gperftools via homebrew. In addition, I found this stackoverflow question showing this:
Then I ran pprof to generate the output:
[hidden ~]$ pprof --text ./a.out cpu.profile
Using local file ./a.out.
Using local file cpu.profile.
Removing __sigtramp from all stack traces.
Total: 282 samples
107 37.9% 37.9% 107 37.9% 0x000000010d72229e
16 5.7% 43.6% 16 5.7% 0x000000010d721a5f
12 4.3% 47.9% 12 4.3% 0x000000010d721de8
...
Running that command (without any of the prior steps) gets me this:
[hidden]$ pprof --text ./a.out cpu.profile
Using remote profile at ./a.out.
Failed to get the number of symbols from http://cpu.profile/pprof/symbol
Why does it try to access an internet site on my machine and a local file on his/hers?
Attempting to link lib profiler as a dry run with g++ gets me:
[hidden]$ g++ -l libprofiler
ld: library not found for -llibprofiler
clang: error: linker command failed with exit code 1 (use -v to see invocation)
I have looked at the man pages, the help option text, the official online guide, blog posts, and many other sources.
I am so confused right now. Can someone help me use gperftools?
The result of my conversation with #osgx was this script. I tried to clean it up a bit. It likely contains quite a few unnecessary options too.
The blog post https://dudefrommangalore.wordpress.com/2012/02/09/profiling-c-code-using-google-performance-tools/ "Profiling C++ code using Google Performance Tools" 2012 by dudefrommangalore missed the essential step.
You should link your program (which you want to be profiled) with cpu profiler library of gperftools library.
Check official manual: http://goog-perftools.sourceforge.net/doc/cpu_profiler.html, part "Linking in the Library"
add -lprofiler to the link-time step for your executable. (It's also probably possible to add in the profiler at run-time using LD_PRELOAD, but this isn't necessarily recommended.)
Second step is to collect the profile, run the code with profiling enabled. In linux world it was done by setting controlling environment variable CPUPROFILE before running:
CPUPROFILE=name_of_profile ./program_to_be_profiled
Third step is to use pprof (google-pprof in ubuntu world). Check that there is not-empty name_of_profile profile file generated; it there is no such file, pprof will try to do remote profile fetch (you see output of such try).
pprof ./program_to_be_profiled name_of_profile
First you need to run your program with profiling enabled.
This is usually first linking your program with libprofiler and then running it with CPUPROFILE=cpu.profile.
I.e.
$ CPUPROFILE=cpu.profile my_program
I think that later step is what you have been missing.
The program will create this cpu.profile file when it exits. And then you can use pprof (preferably from github.com/google/pprof) on it to visualize/analyze.
I want to compile a source code but I have trouble in compile.
cc -O2 -Olimit 2000 -g -migrate -assume -Zp1 noaligned_objects ...
cc: error: 2000: No such file or directory
cc: error: noaligned_objects: No such file or directory
cc: error: unrecognized command line option ‘-migrate’
cc: error: unrecognized command line option ‘-assume’
cc: error: unrecognized command line option ‘-Zp1’
Start with compiling it with no system-specific flags (i.e. by using gcc possibly with -I, -L, and -l flags and nothing else). If the program in question is portable enough, then it will be a matter of getting all dependencies available for it.
Once you are able to build it, see if it runs as expected (ignore performance). If it doesn't, that would be a good time to look at the flags you used on DEC to see if it requires any special treatment when building. This is where you either make the program portable or try to get the equivalent behavior using gcc on the target architecture of your choice.
Finally, once the program builds and runs, that would be a good time to see if you want to use any optimization flags (hint: you don't have to. If it runs fine, leave it the way it is).
I am having trouble compiling Fortran code with references to DISLIN. I have downloaded DISLIN from the website, unzipped the file and ran the setup. I have added an environment variable called DISLIN (C:\dislin) and added C:\dislin\win to the PATH section of my system variables.
I am trying to compile some example code of the DISLIN website which includes line
USE DISLIN
I am using a MinGW shell to compile with command gfortran -o progrname -ldislin EX11_1.f90 and am getting the following error:
Fatal Error: Cant open module file 'dislin.mod' for reading at (1): No such file or directory.
I have tried changing the variable path and even moving the dislin.mod file (which is there) but still get the same message.
Ok I fixed this problem so thought I come back and post what worked for me incase any one else needs it...
Install both DISLIN and MinGW on the c drive
Copy disgf.a from /c/dislin and dislin.f90 from /c/dislin/gf into the directory containing your fortran files
(for me this is /c/MinGW/pnote)
Using the MinGW shell navigate to you files: cd /c/MinGW/pnote
compile dislin.f90 and your fortran program: gfortran -c dislin.f90 progName.f90 (dislin.f90 obviously only needs to be done once)
link libraries etc and compile: gfortran progName.o disgf.a -luser32 -lgdi32 -lopengl32 -o exeName
'run' exeName
You probably need to specify the path to the DISLIN module files:
gfortran EX11_1.f90 -o progrname -ldislin -I/path/to/DISLIN/modules
and, if not already configured like described here, also the path to the library itself:
gfortran EX11_1.f90 -o progrname -ldislin -I/path/to/DISLIN/modules \
-L/path/to/DISLIN/library
They provide a batch file (windows) to do the compiling and linking for you.
f90link -c My_Program
This is located in c:\dislin\Win
Also, if you are having trouble with the dislin.mod file which resides in c:\dislin\gf then recompile that with the -c compile option. I found all of this info in c:\dislin\readme.inf
near as I can tell (Jan 2018) dislin (64 bit) fails miserably with gfortran 7.2, period; and probably with many other newer compilers.
When trying to link, gfortran 7 says 'dislin.mod' is an unrecognizable format.
I think this program is highly dependent on exactly correct version synchronization - something that renders such software useless imho after many years in research.
and no, the correctness of various 'paths' seems not to help.
after all, gnuplot works, "at all". Not sure why I spent so much time on brand x.
jrc