HDF5 lib from Visual Studio

During October last year, my work involved using HDF library with FORTRAN and C and use them to store mounds of data other systems were generating.

The first step was to use the library with visual studio 2008 in windows. Companywide HDF5 had many users in Linux cluster but no formal implementation was available to use in visual studio. While that made the library available but building, a program using them in visual studio was a different matter. I faced couple of issues and with much googling and stack overflowing, solved them, here is a running note I took for one of the issue, just in case someone else is in the same situation.

Hope this helps.

1>libhdf5.lib(H5I.c.obj) : error LNK2001: unresolved external symbol _forceCRTManifestCUR

1>libhdf5.lib(H5.c.obj) : error LNK2001: unresolved external symbol _forceCRTManifestCUR

1>libhdf5.lib(H5D.c.obj) : error LNK2001: unresolved external symbol _forceCRTManifestCUR

1>libhdf5.lib(H5F.c.obj) : error LNK2001: unresolved external symbol _forceCRTManifestCUR

1>libhdf5.lib(H5S.c.obj) : error LNK2001: unresolved external symbol _forceCRTManifestCUR

From: https://social.msdn.microsoft.com/Forums/vstudio/en-US/af6796af-a1bf-4904-9923-15101956d882/linking-error-with-vc9-error-lnk2001-unresolved-external-symbol-forcecrtmanifestcur?forum=vcgeneral

  • The various header files associated with the visual C++ runtime embed a number of directives into the compiled code. This power used to be used for good: appropriate #pragma’s could ensure that the resulting .lib file automatically had a dependency on the correct runtime libraries.

    However, a kind of dependency ____ comes about when one tries to mix projects built with different build settings in the same version of dev studio, and becomes even worse when pre-built libs made by another version of Dev Studio are used.

    The best thing to do, frankly, would be to rebuild your .libs in the same version of Dev Studio. There are some project settings that can be used when building a .lib that can ‘sanitize it’ a bit and make it’s use more compatible with different versions of dev studio – libraries should generally be built with the multi threaded runtime selected (NOT the DLL runtime) and the option “Omit Default Library Names” selected.

    In this case, __forceCRTManifestCUR, is a result of a #pragma comment(linker, “/INCLUDE=__forceCRTManifestCUR”) directive in one of the c-runtime header files.

    You can work around this by simply including a like like this in your main.cpp file:

    int __forceCRTManifestCUR=0;

    Doing this will “defeat” an attempt by the headers to get a manifest dependency to the “current” version of the CRT dlls embedded – but don’t worry – the correct CRT manifest is already specified correctly using a different mechanism, so you can generally quite safely define this symbol (by declaring it as an int or anything really) without causing any problems for the project.

The Best Debugging Tool of All

Rob Pike (one of the authors of the Go language) has this to say on debugging…..:

A year or two after I’d joined the Labs, I was pair programming with Ken Thompson on an on-the-fly compiler for a little interactive graphics language designed by Gerard Holzmann. I was the faster typist, so I was at the keyboard and Ken was standing behind me as we programmed. We were working fast, and things broke, often visibly—it was a graphics language, after all. When something went wrong, I’d reflexively start to dig in to the problem, examining stack traces, sticking in print statements, invoking a debugger, and so on. But Ken would just stand and think, ignoring me and the code we’d just written. After a while I noticed a pattern: Ken would often understand the problem before I would, and would suddenly announce, “I know what’s wrong.” He was usually correct. I realized that Ken was building a mental model of the code and when something broke it was an error in the model. By thinking about *how* that problem could happen, he’d intuit where the model was wrong or where our code must not be satisfying the model.

Ken taught me that thinking before debugging is extremely important. If you dive into the bug, you tend to fix the local issue in the code, but if you think about the bug first, how the bug came to be, you often find and correct a higher-level problem in the code that will improve the design and prevent further bugs.

I recognize this is largely a matter of style. Some people insist on line-by-line tool-driven debugging for everything. But I now believe that thinkingwithout looking at the code—is the best debugging tool of all, because it leads to better software.

Error spawning ‘cmd.exe’ and how to solve it


Yes I know the world have moved beyond visual studio 2013, but at office we are stuck with Visual studio 8 and after working for some time, it spits the following error.


Error 4 Error spawning ‘cmd.exe’.

Then, I have to close the visual studio and restart again. This works. Although not ideal, I was happy doing this as writing the method was more important than tinkering with visual studio.

Last week I had enough and decided to google and get this sorted.. So here’s the solution from ever useful stack overflow that worked like a charm for me.


Just open Tools -> Options -> Projects and Solutions -> VC++ Directories

and add these lines :


Now back to work!!!

Solving ‘ld: library not found’ issues after upgrading to OS X El Capitain


Upgrading to a new OS is always exciting, but if one uses a system for development, then its not always smooth.

Here’s one issue i recently faced after upgrading to OS X El Capitain.

I was recently converting a fortran program to python on macbook using the f2py and got the following error.

ld: library not found for -lbundle1.o

The code complied but the bundle library was missing during linking , this code worked last time I did it, so the suspect was the new OS X El Capitain.

More specifically the suspect was the Xcode library, so I reinstalled the developer tools using the command:

xcode-select –install

Took 15 minutes but after those minutes, faced a new problem, now gcc_s.10.5 library was missing..  

ld: library not found for -lgcc_s.10.5

This was more tricky than the first problem but quickly found this fix from here.

cd /usr/local/lib

sudo ln -s ../../lib/libSystem.B.dylib libgcc_s.10.5.dylib

These two problems solved. Now back to work. 

GDB commands by function

In office, doing a lot of linux code debugging. Missing the luxury of visual studio. Fed up with having multiple print statements all over the code, have switched to gdb and this excellent text file is the best ready reference I found on gdb commands.

Great resource if you are stuck with debugging in linux. [yes, yes, can’t install anything on the company system, if a big process all together!!!]

from: http://web.cecs.pdx.edu/~jrb/ by James R. Binkley

GDB commands by function - simple guide
More important commands have a (*) by them.

% gdb -help         	print startup help, show switches
*% gdb object      	normal debug 
*% gdb object core 	core debug (must specify core file)
%% gdb object pid  	attach to running process
% gdb        		use file command to load object 

*(gdb) help        	list command classes
(gdb) help running      list commands in one command class
(gdb) help run        	bottom-level help for a command "run" 
(gdb) help info         list info commands (running program state)
(gdb) help info line    help for a particular info command
(gdb) help show         list show commands (gdb state)
(gdb) help show commands        specific help for a show command

*(gdb) break main       set a breakpoint on a function
*(gdb) break 101        set a breakpoint on a line number
*(gdb) break basic.c:101        set breakpoint at file and line (or function)
*(gdb) info breakpoints        show breakpoints
*(gdb) delete 1         delete a breakpoint by number
(gdb) delete        	delete all breakpoints (prompted)
(gdb) clear             delete breakpoints at current line
(gdb) clear function    delete breakpoints at function
(gdb) clear line        delete breakpoints at line
(gdb) disable 2         turn a breakpoint off, but don't remove it
(gdb) enable 2          turn disabled breakpoint back on
(gdb) tbreak function|line        set a temporary breakpoint
(gdb) commands break-no ... end   set gdb commands with breakpoint
(gdb) ignore break-no count       ignore bpt N-1 times before activation
(gdb) condition break-no expression         break only if condition is true
(gdb) condition 2 i == 20         example: break on breakpoint 2 if i equals 20
(gdb) watch expression        set software watchpoint on variable
(gdb) info watchpoints        show current watchpoints

Running the program
*(gdb) run        	run the program with current arguments
*(gdb) run args redirection        run with args and redirection
(gdb) set args args...        set arguments for run 
(gdb) show args        show current arguments to run
*(gdb) cont            continue the program
*(gdb) step            single step the program; step into functions
(gdb) step count       singlestep \fIcount\fR times
*(gdb) next            step but step over functions 
(gdb) next count       next \fIcount\fR times
*(gdb) CTRL-C          actually SIGINT, stop execution of current program 
*(gdb) attach process-id        attach to running program
*(gdb) detach        detach from running program
*(gdb) finish        finish current function's execution
(gdb) kill           kill current executing program 

Stack backtrace
*(gdb) bt        	print stack backtrace
(gdb) frame        	show current execution position
(gdb) up        	move up stack trace  (towards main)
(gdb) down        	move down stack trace (away from main)
*(gdb) info locals      print automatic variables in frame
(gdb) info args         print function parameters 

Browsing source
*(gdb) list 101        	list 10 lines around line 101
*(gdb) list 1,10        list lines 1 to 10
*(gdb) list main  	list lines around function 
*(gdb) list basic.c:main        list from another file basic.c
*(gdb) list -        	list previous 10 lines
(gdb) list *0x22e4      list source at address
(gdb) cd dir        	change current directory to \fIdir\fR
(gdb) pwd          	print working directory
(gdb) search regexpr    forward current for regular expression
(gdb) reverse-search regexpr        backward search for regular expression
(gdb) dir dirname       add directory to source path
(gdb) dir        	reset source path to nothing
(gdb) show directories        show source path

Browsing Data
*(gdb) print expression        print expression, added to value history
*(gdb) print/x expressionR        print in hex
(gdb) print array[i]@count        artificial array - print array range
(gdb) print $        	print last value
(gdb) print *$->next    print thru list
(gdb) print $1        	print value 1 from value history
(gdb) print ::gx        force scope to be global
(gdb) print 'basic.c'::gx        global scope in named file (>=4.6)
(gdb) print/x &main     print address of function
(gdb) x/countFormatSize address        low-level examine command
(gdb) x/x &gx        	print gx in hex
(gdb) x/4wx &main       print 4 longs at start of \fImain\fR in hex
(gdb) x/gf &gd1         print double
(gdb) help x        	show formats for x
*(gdb) info locals      print local automatics only
(gdb) info functions regexp         print function names
(gdb) info variables  regexp        print global variable names
*(gdb) ptype name        print type definition
(gdb) whatis expression       print type of expression
*(gdb) set variable = expression        assign value
(gdb) display expression        display expression result at stop
(gdb) undisplay        delete displays
(gdb) info display     show displays
(gdb) show values      print value history (>= gdb 4.0)
(gdb) info history     print value history (gdb 3.5)

Object File manipulation
(gdb) file object      		load new file for debug (sym+exec)
(gdb) file             		discard sym+exec file info
(gdb) symbol-file object        load only symbol table
(gdb) exec-file object 		specify object to run (not sym-file)
(gdb) core-file core   		post-mortem debugging

Signal Control
(gdb) info signals        	print signal setup
(gdb) handle signo actions      set debugger actions for signal
(gdb) handle INT print          print message when signal occurs
(gdb) handle INT noprint        don't print message
(gdb) handle INT stop        	stop program when signal occurs
(gdb) handle INT nostop         don't stop program
(gdb) handle INT pass        	allow program to receive signal
(gdb) handle INT nopass         debugger catches signal; program doesn't
(gdb) signal signo        	continue and send signal to program
(gdb) signal 0        		continue and send no signal to program

Machine-level Debug
(gdb) info registers        	print registers sans floats
(gdb) info all-registers        print all registers
(gdb) print/x $pc        	print one register
(gdb) stepi        		single step at machine level
(gdb) si        		single step at machine level
(gdb) nexti        		single step (over functions) at machine level
(gdb) ni        		single step (over functions) at machine level
(gdb) display/i $pc        	print current instruction in display
(gdb) x/x &gx        		print variable gx in hex
(gdb) info line 22        	print addresses for object code for line 22
(gdb) info line *0x2c4e         print line number of object code at address
(gdb) x/10i main        	disassemble first 10 instructions in \fImain\fR
(gdb) disassemble addr          dissassemble code for function around addr

History Display
(gdb) show commands        	print command history (>= gdb 4.0)
(gdb) info editing       	print command history (gdb 3.5)
(gdb) ESC-CTRL-J        	switch to vi edit mode from emacs edit mode
(gdb) set history expansion on       turn on c-shell like history
(gdb) break class::member       set breakpoint on class member. may get menu
(gdb) list class::member        list member in class
(gdb) ptype class               print class members
(gdb) print *this        	print contents of this pointer
(gdb) rbreak regexpr     	useful for breakpoint on overloaded member name

(gdb) define command ... end        define user command
*(gdb) RETURN        		repeat last command
*(gdb) shell command args       execute shell command 
*(gdb) source file        	load gdb commands from file
*(gdb) quit        		quit gdb

Calling Fortran from C ScreenCast

Was just browsing and came across this website screencast-o-matic.com that allows creating screen cast from web without any installation.

I decided to check this website. And here’s the result.

The video demonstrates calling fortran from c. The fortran is compiled with gfortran and C with Gcc.

Why did I choose this example? Well these two programs were lying around on my netbook’s desktop.

The service is great. It loads a java program and the intuitive GUI is easy to use. Easy upload to YouTube from within the app is topper. 😉

Happy 25th Birthday GNU GCC!

GNU compiler collection or GCC turned 25 last Friday. Gfortran is part of GCC.

To that end, Richard Guenther, who works in tool chain development at Suse Labs, and spends his days working on GCC, sent an email to the GCC development newsgroup to mark this historic occasion. Here a part of it, reprinted, for your reading pleasure.

Today the GCC development team celebrates the 25th anniversary of the GNU Compiler Collection.

When Richard Stallman announced the first public release of GCC in 1987, few could have imagined the broad impact that it has had. It has prototyped many language features that later were adopted as part of their respective standards — everything from "long long" type to transactional memory. It deployed an architecture-neutral automatic vectorization facility, OpenMP, and Polyhedral loop nest optimization. It has provided the toolchain infrastructure for the GNU/Linux ecosystem used everywhere from Google and Facebook to financial markets and stock exchanges. We salute and thank the hundreds of developers who have contributed over the years to make GCC one of the most long-lasting and successful free software projects in the history of this industry.

Whether you know it or not, GCC has probably affected how you go about your daily life with computers.

You might want to read this