MPICH - enable debugging prints from `MPIU_DBG_PRINTF()` - mpich

What is right order of configuring and running MPICH2 or MPICH-3 to enable debugging prints, embedded to code with MPIU_DBG_PRINTF(). I already used --enable-g=dbg,mem,log configure option, and set environment variable MPICH_DBG_OUTPUT to stdout but still have no debug prints from the examples/cpi runs.

you might need to set a few extra environment variables:
MPICH_DBG_LEVEL to VERBOSE
MPICH_DBG_CLASS to ALL
For example:
mpiexec -n 2 -env MPICH_DBG_OUTPUT VERBOSE \
-env MPICH_DBG_CLASS ALL \
-env MPICH_DBG_FILENAME "dbg-%w-%d.log" ./examples/cpi
The wiki has some more information about the other things you can do with the MPICH debugging facility:
https://wiki.mpich.org/mpich/index.php/Debug_Event_Logging

Related

Cannot run Fortify with multi CPU for a C++ project

I have a C++ project setup with CMake, running on Mac. Recently I am looking into adding Fortify to do auto code analyzation. I am using Fortify version 22.1.
After set up the CMake and shell scripts, I found that if I compile with more than one CPU (using -j), the compiler (c++ or g++) will have issues generating the libs. Sometimes it will pass and successfully generate the Fortify output, but others it will just error out. Multi CPUs compile fine for this project without running Fortify.
I also see this error when I compile with Fortify (no matter it success or not):
[error]: Translator execution failed. Please consult the Troubleshooting section of the User Manual.
Translator returned status 1:
error: unable to handle compilation, expected exactly one compiler job in ''
This error always happens after a "Linking CXX xxxxx xxxx". I can't find any documentation about them.
Does anyone know how to solve this? Thank you.
Update more details about my setup:
I use shell files to wrap the sourceanalyzer like this:
#!/bin/bash
exec sourceanalyzer -b MyApp /Library/Developer/CommandLineTools/usr/bin/c++ "$#"
And my CMake setup like this:
if (${ENABLE_FORTIFY} EQUAL 1)
set(CMAKE_CC_COMPILER ${AVSxAppDALDefaultImplementation_SOURCE_DIR}/scripts/fortify-build-cc.sh)
set(CMAKE_CXX_COMPILER ${AVSxAppDALDefaultImplementation_SOURCE_DIR}/scripts/fortify-build-cxx.sh)
endif()
My shell script to run CMake and then to the scan:
cmake $PACKAGEPATH \
...
-DENABLE_FORTIFY="${ENABLE_FORTIFY}"
echo "---BUILDING---"
make release
if [[ $ENABLE_FORTIFY == 1 ]]; then
echo "---RUNNING FORTIFY SCAN---"
sourceanalyzer -b ${CURRENT_PROJECT_NAME} -scan -f fortify_scan_result_${CURRENT_PROJECT_NAME}.txt
fi

How to debug custom kernel with GDB and QEMU [duplicate]

I'm new to kernel development and I would like to know how to run/debug the linux kernel using QEMU and gdb. I'm actually reading Robert Love's book but unfortunately it doesn't help the reader on how to install proper tools to run or debug the kernel... So what I did was to follow this tutorial http://opensourceforu.efytimes.com/2011/02/kernel-development-debugging-using-eclipse/. I'm using eclipse as an IDE to develop on the kernel but I wanted first to get it work under QEMU/gdb. So what I did so far was:
1) To compile the kernel with:
make defconfig (then setting the CONFIG_DEBUG_INFO=y in the .config)
make -j4
2) Once the compilation is over I run Qemu using:
qemu-system-x86_64 -s -S /dev/zero -kernel /arch/x86/boot/bzImage
which launch the kernel in "stopped" state
3) Thus I have to use gdb, I try the following command:
gdb ./vmlinux
which run it correctly but... Now I don't know what to do... I know that I have to use remote debugging on the port 1234 (default port used by Qemu), using the vmlinux as the symbol table file for debugging.
So my question is: What should I do to run the kernel on Qemu, attach my debugger to it and thus, get them work together to make my life easier with kernel development.
I'd try:
(gdb) target remote localhost:1234
(gdb) continue
Using the '-s' option makes qemu listen on port tcp::1234, which you can connect to as localhost:1234 if you are on the same machine. Qemu's '-S' option makes Qemu stop execution until you give the continue command.
Best thing would probably be to have a look at a decent GDB tutorial to get along with what you are doing. This one looks quite nice.
Step-by-step procedure tested on Ubuntu 16.10 host
To get started from scratch quickly I've made a minimal fully automated QEMU + Buildroot example at: https://github.com/cirosantilli/linux-kernel-module-cheat/blob/c7bbc6029af7f4fab0a23a380d1607df0b2a3701/gdb-step-debugging.md Major steps are covered below.
First get a root filesystem rootfs.cpio.gz. If you need one, consider:
a minimal init-only executable image: https://unix.stackexchange.com/questions/122717/custom-linux-distro-that-runs-just-one-program-nothing-else/238579#238579
a Busybox interactive system: https://unix.stackexchange.com/questions/2692/what-is-the-smallest-possible-linux-implementation/203902#203902
Then on the Linux kernel:
git checkout v4.15
make mrproper
make x86_64_defconfig
cat <<EOF >.config-fragment
CONFIG_DEBUG_INFO=y
CONFIG_DEBUG_KERNEL=y
CONFIG_GDB_SCRIPTS=y
EOF
./scripts/kconfig/merge_config.sh .config .config-fragment
make -j"$(nproc)"
qemu-system-x86_64 -kernel arch/x86/boot/bzImage \
-initrd rootfs.cpio.gz -S -s \
-append nokaslr
On another terminal, from inside the Linux kernel tree, supposing you want to start debugging from start_kernel:
gdb \
-ex "add-auto-load-safe-path $(pwd)" \
-ex "file vmlinux" \
-ex 'set arch i386:x86-64:intel' \
-ex 'target remote localhost:1234' \
-ex 'break start_kernel' \
-ex 'continue' \
-ex 'disconnect' \
-ex 'set arch i386:x86-64' \
-ex 'target remote localhost:1234'
and we are done!!
For kernel modules see: How to debug Linux kernel modules with QEMU?
For Ubuntu 14.04, GDB 7.7.1, hbreak was needed, break software breakpoints were ignored. Not the case anymore in 16.10. See also: https://bugs.launchpad.net/ubuntu/+source/qemu-kvm/+bug/901944
The messy disconnect and what come after it are to work around the error:
Remote 'g' packet reply is too long: 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
Related threads:
https://sourceware.org/bugzilla/show_bug.cgi?id=13984 might be a GDB bug
Remote 'g' packet reply is too long
http://wiki.osdev.org/QEMU_and_GDB_in_long_mode osdev.org is as usual an awesome source for these problems
https://lists.nongnu.org/archive/html/qemu-discuss/2014-10/msg00069.html
nokaslr: https://unix.stackexchange.com/questions/397939/turning-off-kaslr-to-debug-linux-kernel-using-qemu-and-gdb/421287#421287
Known limitations:
the Linux kernel does not support (and does not even compile without patches) with -O0: How to de-optimize the Linux kernel to and compile it with -O0?
GDB 7.11 will blow your memory on some types of tab completion, even after the max-completions fix: Tab completion interrupt for large binaries Likely some corner case which was not covered in that patch. So an ulimit -Sv 500000 is a wise action before debugging. Blew up specifically when I tab completed file<tab> for the filename argument of sys_execve as in: https://stackoverflow.com/a/42290593/895245
See also:
https://github.com/torvalds/linux/blob/v4.9/Documentation/dev-tools/gdb-kernel-debugging.rst official Linux kernel "documentation"
Linux kernel live debugging, how it's done and what tools are used?
When you try to start vmlinux exe using gdb, then first thing on gdb is to issue cmds:
(gdb) target remote localhost:1234
(gdb) break start_kernel
(continue)
This will break the kernel at start_kernel.
BjoernID's answer did not really work for me. After the first continuation, no breakpoint is reached and on interrupt, I would see lines such as:
0x0000000000000000 in ?? ()
(gdb) break rapl_pmu_init
Breakpoint 1 at 0xffffffff816631e7
(gdb) c
Continuing.
^CRemote 'g' packet reply is too long: 08793000000000002988d582000000002019[..]
I guess this has something to do with different CPU modes (real mode in BIOS vs. long mode when Linux has booted). Anyway, the solution is to run QEMU first without waiting (i.e. without -S):
qemu-system-x86_64 -enable-kvm -kernel arch/x86/boot/bzImage -cpu SandyBridge -s
In my case, I needed to break at something during boot, so after some deciseconds, I ran the gdb command. If you have more time (e.g. you need to debug a module that is loaded manually), then the timing doesn't really matter.
gdb allows you to specify commands that should be run when started. This makes automation a bit easier. To connect to QEMU (which should now already be started), break on a function and continue execution, use:
gdb -ex 'target remote localhost:1234' -ex 'break rapl_pmu_init' -ex c ./vmlinux
As for me the best solution for debugging the kernel - is to use gdb from Eclipse environment. You should just set appropriate port for gdb (must be the same with one you specified in qemu launch string) in remote debugging section. Here is the manual:
http://www.sw-at.com/blog/2011/02/11/linux-kernel-development-and-debugging-using-eclipse-cdt/
On Linux systems, vmlinux is a statically linked executable file that contains
the Linux kernel in one of the object file formats supported by Linux, which
includes ELF, COFF and a.out. The vmlinux file might be required for kernel
debugging, symbol table generation or other operations, but must be made
bootable before being used as an operating system kernel by adding a multiboot
header, bootsector and setup routines.
An image of this initial root file system must be stored somewhere accessible
by the Linux bootloader to the boot firmware of the computer. This can be the
root file system itself, a boot image on an optical disc, a small partition on
a local disk (a boot paratition, usually using ext4 or FAT file systems), or a
TFTP server (on systems that can boot from Ethernet).
Compile linux kernel
Build the kernel with this series applied, enabling CONFIG_DEBUG_INFO (but leave CONFIG_DEBUG_INFO_REDUCED off)
https://www.kernel.org/doc/html/latest/admin-guide/README.html
https://wiki.archlinux.org/index.php/Kernel/Traditional_compilation
https://lwn.net/Articles/533552/
Install GDB and Qemu
sudo pacman -S gdb qemu
Create initramfs
#!/bin/bash
# Os : Arch Linux
# Kernel : 5.0.3
INIT_DIR=$(pwd)
BBOX_URL="https://busybox.net/downloads/busybox-1.30.1.tar.bz2"
BBOX_FILENAME=$(basename ${BBOX_URL})
BBOX_DIRNAME=$(basename ${BBOX_FILENAME} ".tar.bz2")
RAM_FILENAME="${INIT_DIR}/initramfs.cpio.gz"
function download_busybox {
wget -c ${BBOX_URL} 2>/dev/null
}
function compile_busybox {
tar xvf ${BBOX_FILENAME} && cd "${INIT_DIR}/${BBOX_DIRNAME}/"
echo "[*] Settings > Build options > Build static binary (no shared libs)"
echo "[!] Please enter to continue"
read tmpvar
make menuconfig && make -j2 && make install
}
function config_busybox {
cd "${INIT_DIR}/${BBOX_DIRNAME}/"
rm -rf initramfs/ && cp -rf _install/ initramfs/
rm -f initramfs/linuxrc
mkdir -p initramfs/{dev,proc,sys}
sudo cp -a /dev/{null,console,tty,tty1,tty2,tty3,tty4} initramfs/dev/
cat > "${INIT_DIR}/${BBOX_DIRNAME}/initramfs/init" << EOF
#!/bin/busybox sh
mount -t proc none /proc
mount -t sysfs none /sys
exec /sbin/init
EOF
chmod a+x initramfs/init
cd "${INIT_DIR}/${BBOX_DIRNAME}/initramfs/"
find . -print0 | cpio --null -ov --format=newc | gzip -9 > "${RAM_FILENAME}"
echo "[*] output: ${RAM_FILENAME}"
}
download_busybox
compile_busybox
config_busybox
Boot Linux Kernel With Qemu
#!/bin/bash
KER_FILENAME="/home/debug/Projects/kernelbuild/linux-5.0.3/arch/x86/boot/bzImage"
RAM_FILENAME="/home/debug/Projects/kerneldebug/initramfs.cpio.gz"
qemu-system-x86_64 -s -kernel "${KER_FILENAME}" -initrd "${RAM_FILENAME}" -nographic -append "console=ttyS0"
$ ./qemuboot_vmlinux.sh
SeaBIOS (version 1.12.0-20181126_142135-anatol)
iPXE (http://ipxe.org) 00:03.0 C980 PCI2.10 PnP PMM+07F92120+07EF2120 C980
Booting from ROM...
Probing EDD (edd=off to disable)... o
[ 0.019814] Spectre V2 : Spectre mitigation: LFENCE not serializing, switching to generic retpoline
can't run '/etc/init.d/rcS': No such file or directory
Please press Enter to activate this console.
/ # uname -a
Linux archlinux 5.0.3 #2 SMP PREEMPT Mon Mar 25 10:27:13 CST 2019 x86_64 GNU/Linux
/ #
Debug Linux Kernel With GDB
~/Projects/kernelbuild/linux-5.0.3 ➭ gdb vmlinux
...
(gdb) target remote localhost:1234
Remote debugging using localhost:1234
0xffffffff89a4b852 in ?? ()
(gdb) break start_kernel
Breakpoint 1 at 0xffffffff826ccc08
(gdb)
Display all 190 possibilities? (y or n)
(gdb) info functions
All defined functions:
Non-debugging symbols:
0xffffffff81000000 _stext
0xffffffff81000000 _text
0xffffffff81000000 startup_64
0xffffffff81000030 secondary_startup_64
0xffffffff810000e0 verify_cpu
0xffffffff810001e0 start_cpu0
0xffffffff810001f0 __startup_64
0xffffffff81000410 pvh_start_xen
0xffffffff81001000 hypercall_page
0xffffffff81001000 xen_hypercall_set_trap_table
0xffffffff81001020 xen_hypercall_mmu_update
0xffffffff81001040 xen_hypercall_set_gdt
0xffffffff81001060 xen_hypercall_stack_switch
0xffffffff81001080 xen_hypercall_set_callbacks
0xffffffff810010a0 xen_hypercall_fpu_taskswitch
0xffffffff810010c0 xen_hypercall_sched_op_compat
0xffffffff810010e0 xen_hypercall_platform_op

are there options to speed up dpkg-buildpackage

Im back porting ffmpeg to an older version of debian.
everything is going well, but its so slow.
I am running dpkg-buildpackage -us -uc
with a debian rules file that looks like this:
#!/usr/bin/make -f
%:
dh $#
override_dh_auto_configure:
./configure
I notice, this is only processing on 1 core.
is there anything like make -j 4 that I could use to speed this up?
I've been using this guide, but i don't see anything for speeding up the build step
https://www.debian.org/doc/manuals/maint-guide/
Sure, you can use -j 4 as an argument to dpkg-buildpackage. It is documented in the man page. The relevant section is:
-jjobs Number of jobs allowed to be run simultaneously, equivalent to
the make(1) option of the same name. Will add itself to
the MAKEFLAGS environment variable, which should cause all
subsequent make invocations to inherit the option. Also adds
parallel=jobs to the DEB_BUILD_OPTIONS environment variable which
allows debian/rules files to use this information for their own
purposes. The parallel=jobs in DEB_BUILD_OPTIONS environment
variable will override the -j value if this option is given.

how to set dynamic link library path and environment variable for a process in valgrind

I need to set LD_LIBRARY_PATH, LD_PRELOAD and some environment variables for a process while running and detect memory leaks with Valgrind.
Can anyone suggest a way to set or pass these variable for a process in valgrind?.
I've run into a similar issue, trying to run valgrind on programs that need libraries incompatible with the ones valgrind uses, and have been using:
valgrind --trace-children=yes env LD_LIBRARY_PATH=your_library_path OTHER_VAR=foo your_program arg1 arg2...
env sets up the environment and then execs your_program. We need to pass the --trace-children=yes argument to valgrind in order for it to continue to trace through the exec syscall. Without --trace-children=yes set, valgrind will stop tracing at the exec and you won't get any useful output from valgrind on your_program.
One potential downside to this approach is that valgrind might report any memory issues in env. I haven't seen any false positives from this source (env is not a very complicated program), but it could happen.
I haven't tried this with LD_PRELOAD though (it hasn't come up for my use-case yet). Valgrind does set LD_PRELOAD, so you might have to do something like:
valgrind --trace-children=yes env LD_PRELOAD=$LD_PRELOAD:your_preload your_program
What is wrong with the standard mechanisms? These include:
LD_LIBRARY_PATH=$new_libpath LD_PRELOAD=$new_preload OTHERVAR=otherval valgrind your.program arg1 …
Or:
env LD_LIBRARY_PATH=$new_libpath \
LD_PRELOAD=$new_preload \
OTHERVAR=otherval \
valgrind ./your.program arg1 …
Or:
export LD_LIBRARY_PATH=$new_libpath
export LD_PRELOAD=$new_preload
export OTHERVAR=otherval
valgrind ./your.program arg1 …
The advantage of the first two mechanisms is that it doesn't affect the working environment of your shell. The advantage of the last mechanism is that it does affect the working environment of your shell (which makes it easier to run valgrind the next time — you don't have to remember to find the command with the environment in your history).

How to run a linux script before launching gdb debugging in Eclipse

How do I give commands to run before starting gdb debugging in Eclipse ?
Actually I want to execute few scripts that set environment variables (export vars) and execute a bunch of other programs before gdb process is launched from eclipse to debug my program.
I tried doing the following in debugger tab option:
<command> && <path-to-gdb-executable>
But I got the error that eclipse cannot execute gdb as given in above statement.
Please help - I actually want to execute a script called "before-launch-commands.sh" before debugging is started by gdb. I am trying to execute a cpp program under eclipse kepler.
Thanks.
The Eclipse Debug Configurations can already setup environment variables for you. I'm going to assume that that isn't sufficient, or you'd have already done it.
The first thing to do is create a new script, wrapped-gdb.sh:
#!/bin/sh
# Export any variables we need.
# Note that '.' (dot) is like an "include" statement.
. /path/to/before-launch-commands.sh
# Run GDB using the parameters passed in
exec /path/to/gdb "$#"
Next, set that script executable:
chmod +x /path/to/wrapped-gdb.sh
Finally, go to the Debugger tab in the debug configuration dialog, and in the box marked "GDB Debugger" enter /path/to/wrapped-gdb.sh.
When you launch your debug session it should now Do The Right Thing.