Python module error in Mac OS X Lion

[shhong]

In Mac OS 10.7 aka Lion, importing the python module causes an exception as follows: (NEURON version: 536:c4eed98bb84b, Python: 2.7.1, compiler: i686-apple-darwin11-llvm-gcc-4.2)

Code: Select all

In [1]: import neuron
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/Users/shhong/<ipython-input-1-861d48cbe3e0> in <module>()
----> 1 import neuron

/Library/Python/2.7/site-packages/neuron/__init__.py in <module>()
     79 except:
     80   #Python3.1 extending needs to look into the module explicitly

---> 81   import neuron.hoc
     82
     83 import nrn

ImportError: dlopen(/Library/Python/2.7/site-packages/neuron/hoc.so, 2): Symbol not found: _environ
  Referenced from: /Applications/NEURON/nrn/x86_64/lib/liboc.0.dylib
  Expected in: flat namespace
in /Applications/NEURON/nrn/x86_64/lib/liboc.0.dylib


This is because Mac OS X handles environ in a non-POSIX-standard way, and the environ pointer cannot be used in dynamic libraries but should be read via _NSGetEnviron(). Here is the patch:

Code: Select all

diff -r c4eed98bb84b src/ivoc/ivocmain.cpp
--- a/src/ivoc/ivocmain.cpp   Mon Aug 15 10:58:56 2011 -0400
+++ b/src/ivoc/ivocmain.cpp   Tue Aug 16 03:09:24 2011 +0900
@@ -12,17 +12,21 @@ extern "C" {
   void hoc_main1_init(char*, char**);
}
#endif

#include <stdio.h>
#include <stdlib.h>
#if HAVE_UNISTD_H
#include <unistd.h>
+#if !defined (__APPLE__)
extern char** environ;
+#else
+#include <crt_externs.h>
+#endif
#endif

#if HAVE_IV
#ifdef WIN32
#include <IV-Win/MWlib.h>
void iv_display_scale(float);
#endif

@@ -466,19 +470,22 @@ int ivocmain (int argc, char** argv, cha
      setenv("NEURONHOME", NEURON_DATA_DIR, 1);
      neuron_home = NEURON_DATA_DIR;
#else
#error "I don't know how to set environment variables."
// Maybe in this case the user will have to set it by hand.
#endif
      // putenv and setenv may invalidate env but we no longer
      // use it so following should not be needed
-#if HAVE_UNISTD_H
+#if HAVE_UNISTD_H && !defined(__APPLE__)
      env = environ;
#endif
+#if defined (__APPLE__)
+    env = (*_NSGetEnviron());
+#endif
   }

#else // Not unix:
   neuron_home = getenv("NEURONHOME");
   if (!neuron_home) {
      setneuronhome((argc > 0)?argv[0]:0);
   }
   if (!neuron_home) {
diff -r c4eed98bb84b src/oc/parallel.c
--- a/src/oc/parallel.c   Mon Aug 15 10:58:56 2011 -0400
+++ b/src/oc/parallel.c   Tue Aug 16 03:09:24 2011 +0900
@@ -5,16 +5,20 @@
   #define WIN32 1
#endif

#if !OCSMALL
#include <stdlib.h>
#if HAVE_UNISTD_H
#include <unistd.h>
#endif
+#if defined(__APPLE__)
+#include <crt_externs.h>
+#endif
+
#include "hoc.h"
#include "parse.h" /* OBJECTVAR */

static int parallel_seen;

static double *pval; /* pointer to loop counter value */
static double end_val; /* value to assign loop counter upon completion of loop */

@@ -240,20 +244,25 @@ save_parallel_argv(argc, argv)
     }
     *pnt = '\0'; /* place extra '\0' at end */
#endif
#endif
}

save_parallel_envp() {
#if LINDA
+#if !defined(__APPLE__)
   extern char** environ;
+   char** envp = environ;
+#endif
+#if defined(__APPLE__)
+  char** envp = (*_NSGetEnviron());
+#endif
    char *pnt;
     int j;
-   char** envp = environ;

     /* count how long the block of memory should be */
     for (j = 0; envp[j]; j++) {
   pnt = envp[j];
   while (*pnt++) { senvp++; }
   senvp++; /* add room for '\0' */
     }

diff -r c4eed98bb84b src/oc/plot.c
--- a/src/oc/plot.c   Mon Aug 15 10:58:56 2011 -0400
+++ b/src/oc/plot.c   Tue Aug 16 03:09:24 2011 +0900
@@ -1,9 +1,10 @@
#include <../../nrnconf.h>
+ 
/* /local/src/master/nrn/src/oc/plot.c,v 1.7 1999/06/22 12:51:55 hines Exp */
/*
plot.c,v
  * Revision 1.7  1999/06/22  12:51:55  hines
  * a work around for LINUX installation problem with old style x graph
  * using plot (just not compile it)
  *
  * Revision 1.6  1999/05/11  13:56:03  hines
@@ -203,18 +204,23 @@ plot.c,v
#include <stdio.h>
#include <string.h>

#if defined(__MINGW32__)
extern char** _environ;
#else //!defined(__MINGW32__)
#if HAVE_UNISTD_H
#include <unistd.h>
+#if !defined(__APPLE__)
extern char** environ;
#endif
+#if defined(__APPLE__)
+#include <crt_externs.h>
+#endif
+#endif
#endif //defined(__MINGW32__)

#if DOS
#include <graphics.h>
#include <dos.h>
#endif
#if defined(GRX)
#define DOS 1
@@ -503,16 +509,19 @@ hoc_outtext(s) char* s; {
#endif

initplot()
{
   int i;
#if defined(__MINGW32__)
   char** environ=_environ;
#endif
+#if defined (__APPLE__)
+  char** environ=(*_NSGetEnviron());
+#endif
#if defined(__TURBOC__)
   graphdev = 0;
#else
#if NeXTstep
   graphdev = NX;
#else
   graphdev = SSUN;
   for (i = 0; environ[i] != NULL; i++)
diff -r c4eed98bb84b src/oc/system.c
--- a/src/oc/system.c   Mon Aug 15 10:58:56 2011 -0400
+++ b/src/oc/system.c   Tue Aug 16 03:09:24 2011 +0900
@@ -55,16 +55,20 @@ Supporting OS subroutines required: <<_e

#include <errno.h>
#include <stddef.h>
#include <stdlib.h>
#include <unistd.h>
#include <_syslist.h>
#include <reent.h>

+#if defined (__APPLE__)
+#include <crt_externs.h>
+#endif
+
#if defined (unix) || defined (__CYGWIN__)
static int do_system ();
#endif

int
_system_r (ptr, s)
      struct _reent *ptr;
      _CONST char *s;
@@ -103,24 +107,29 @@ _system_r (ptr, s)
int
system (s)
      _CONST char *s;
{
   return _system_r (_REENT, s);
}

#endif
-
+
#if defined (unix) && !defined (__CYGWIN__) && !defined(__rtems__)
+#if !defined(__APPLE__)
extern char **environ;

/* Only deal with a pointer to environ, to work around subtle bugs with shared
    libraries and/or small data systems where the user declares his own
    'environ'.  */
static char ***p_environ = &environ;
+#endif
+#if defined(__APPLE__)
+static char ***p_environ = _NSGetEnviron();
+#endif

static int
do_system (ptr, s)
      struct _reent *ptr;
      _CONST char *s;
{
   char *argv[4];
   int pid, status;


[khosra]

Thanks for your post. I am having this issue with Lion whereas others seem not to.

How do you apply this patch? I am not sure if it's my unfamiliarity with patch or another issue that is causing the patch not to be applied.

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% cd $HOME/neuron/nrn
% patch --dry-run -p1 < environ_patch

patching file src/ivoc/ivocmain.cpp
patch: **** malformed patch at line 6: }


[pbmanis]

I received the same error with the patch. However, I was able to manually edit the files (ivocmain.cpp, plot.c, parallel.c ,and system.c) to make the changes indicated in the patch - add the lines with "+" in front of them where indicated, and remove any lines with "-" in front of them. There were only 2 or 3 places to edit in each file, so it wasn't hard.

Everything then compiled perfectly, and is working great with Python 2.7.2.5 from Active State (Community edition).

--Paul

[ted]

Thanks, Paul, that's a useful suggestion.

[selfdestructo]

Hi,
Will sshong's patch make it into the alpha-repository?
I'm experiencing the same problem here and had to roll back to my previous install;
NEURON -- VERSION 7.2 (504:f8e1ebea86e4) f8e1ebea86e4

Then, it loads just fine

Best,
Espen

[hines]

I'll be pushing this to the repository sometime this week. Hopefully tonight.

[hines]

I've learned that one cannot easily copy/paste code fragments from the forum
into a file and then use it as a patch. If someone will send me an email with an
attachment with the proper patch contents that would be very helpful.
Otherwise, I'll wait til next week when I get back to my mac so I can do it manually.
(send to michael dot hines at yale dot edu)

[selfdestructo]

I'm not sure if it helps or not, but I was able to use the patch as copied and paste with the --ignore-whitespace flag to rev 536, i.e;

Code: Select all

hg update -r 536:c4eed98bb84b
patch -Np1 --ignore-whitespace < environ_patch


This will build correctly for me using

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sh build.sh
./configure --prefix=/Applications/NEURON-7.2/nrn --with-iv=/Applications/NEURON-7.2/iv \
    --with-x --x-includes=/usr/X11/include/ --x-libraries=/usr/X11/lib/ \
    --with-nrnpython=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python \
    --host=x86_64-apple-darwin10.7.0 --build=x86_64-apple-darwin10.7.0
make
sudo make install
sudo make after_install
cd src/nrnpython
sudo python setup.py install


Updating to the latest revision would fail to build though during make.

[hines]

I couldn't get the patch to apply so manually added the changes. Same issues with line 6 as mentioned by others. Anyway, see
http://www.neuron.yale.edu/hg/neuron/nr ... 8a73adcc53
Many thanks to shhong.
Of course, let me know if some typo has crept in.

[selfdestructo]

Works for me!
Espen.