How to enable hibernate on Manjaro

 To enable hibernate:

1. >sudo nano /etc/mkinitcpio.conf 

Add "resume" at the end of HOOKS=()

HOOKS=(base udev autodetect kms modconf block keyboard keymap consolefont plymouth filesystems fsck resume)
 

2.  sudo mkinitcpio -P #careful with this as if you get wrong mkinitcpio.conf it can ruin your system, it did for mine and I had to chroot it

3. In case you don't have swap entry in your fstab (but you have it otherwise) add it with:

>sudo blkid

Copy the #id from the line saying swap

>sudo nano /etc/fstab

add:

UUID=#id none swap defaults 0 0

where #id is the uuid from blkid

4.  >sudo nano /etc/default/grub

add at the end of GRUB_CMDLINE_LINUX_DEFAULT the resume=UUID=#id

GRUB_CMDLINE_LINUX_DEFAULT="quiet splash udev.log_priority=3 resume=UUID=#id"

(make sure that #id in blkid, fstab and grub is the same!)

5. >sudo update-grub

And now it seems that hibernate is working. Yay.

How to recover system after it crashes during update

Today was a crazy day. I wanted to update the system to see if the new ollama is available and in the middle of the update, I got kernel panic and everything froze. Upon restart, Manjaro 6.89 said kernel doesn't exist and Manjaro 6.77 was starting only in terminal with alt+f2 with no wifi. It was a disaster. 

First, I found that internet from the phone trough usb works, but that didn't help as it would download the packages and then complain about the wrong PGP signature.

Here's a list of the problems I had:

1) my konsole was giving me the errors in Bulgarian, which showed up like white squares making them unreadable. 

I fixed that by changing:

>localectl set-locale LANG=en_US.UTF-8

and then I commented >#bg_BG.UTF-8 UTF-8

in

sudo nano /etc/locale.gen

and now I have a line: LANG=en_US.UTF-8

in sudo nano /etc/locale.conf

2)  I tried installing the kernel without dependencies (as I was convinced that would solve the problem)

>pacman -Sdd linux68 

and that did something random (it installed the files but when I tried to launch it, it couldn't find my hard at all).

3) I did all kinds of attempts to solve the problem with the wrong PGP signature

>bash <(curl -s "https://notabug.org/megavolt/random-scripts/raw/master/fix-gpg-pacman.sh")

the line above was the recommended method, it did something but the problem remained. 

Also this code:

sudo pacman-mirrors -c Global 

sudo cp /etc/pacman.conf /etc/pacman.conf.backup

sudo sed --in-place --regexp-extended 's/^(SigLevel).+$/\1 = Never/g' /etc/pacman.conf

sudo pacman -Syyuu

was supposed to remove the PGP check at all. It might have worked because by then I realised the problem was that pacman was giving an error "package already exist". 

So I made a live usb, backed up the whole home partition (just in case), then I did:

sudo blkid

mount /dev/nvme0n1p6 /mnt

mount -t proc proc /mnt/proc; mount --rbind /sys /mnt/sys; mount --rbind /dev /mnt/dev

pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg -Syu --overwrite "*"

pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg -Syu --overwrite linux68 #not needed but just in case

pacman --root=/mnt --cachedir=/mnt/var/cache/pacman/pkg -Syu  #also just in case

That surprisingly solved all the drama. And my whole day is gone. 

Finally when I restarted into my now working 6.67 linux, I did

>sudo mwid -i linux68

and it found both my Windows and my other kernels and now I had also grub. Yay.

From 0 to working scientific python with pypolychord

This is a brand new Lenovo laptop I got as a backup because my dear Asus got broken. So I got this smaller and weaker but still cute laptop. So I wanted to make this post just to list the quickest install from 0 to a working python file. 

Install python and jupyter

1. pacman -S python3

2. pacman -S jupyter-notebook

Install miniconda3 (instructions here)

3. mkdir -p ~/miniconda3

4. cd ~/miniconda3                                                                                                                                                                                                        
5. wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh

6. bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3

7. ~/miniconda3/bin/conda init bash
 

Then install the packages I need. I'm pretty sure I have an exported file from this environment with the packages but this is the absolute minimum of stuff. 

8.
conda create --name myenv
conda install -n myenv pip
conda install ipykernel
python3 -m ipykernel install --user --name=myenv
pacman -S gcc
pip install wheel
sudo pacman -S make
sudo pacman -S gcc-fortran

(optional conda install libgcc - no idea if this helped)

sudo pacman -S gcc-libs

pip install numpy
pip install git+https://github.com/PolyChord/PolyChordLite@master
conda install matplotlib
pip install getdist

I was getting a persistent error with libstdc++.so.6 (see here for other suggestions), here's what I did (after I installed gcc-libs and gcc-fortran)

sudo find / -name "libstdc++.so*"
conda install -c anaconda libstdcxx-ng
conda update libstdcxx-ng
ls ~/miniconda3/envs/myenv/bin/../lib
cp /usr/lib/libstdc++.so.6.0.32 ~/miniconda3/envs/myenv/bin/../lib 

And then manually removing libstdc++.so.6.0.21 and libstdc++.so.6.0.29

The problem with mpi4py:

I was getting a kernel crash from inside polychord, that I know it's related to mpi4py. So I had to install it. When trying to pip install it, I woul get this error:

"The Open MPI wrapper compiler was unable to find the specified compiler
     x86_64-conda_cos6-linux-gnu-cc in your PATH.
      
     Note that this compiler was either specified at configure time or in
     one of several possible environment variables.
     --------------------------------------------------------------------------
     failure.
     removing: _configtest.c _configtest.o
     error: Cannot compile MPI programs. Check your configuration!!!"

Solving it took a long time and 3 gpts!
 >sudo pacman -S openmpi

>yay -S mpicc
 >yay -S mpich

>echo $PATH
>conda list #look for openmpi - I had it, but obviously not working well enough

x86_64-conda_cos6-linux-gnu-cc

which gcc
/usr/bin/gcc

which mpicc
~/miniconda3/envs/BAO/bin/mpicc
export MPICC=~/miniconda3/envs/BAO/bin/mpicc

>pip install mpi4py #longer output but still and error

The Open MPI wrapper compiler was unable to find the specified compiler
      x86_64-conda_cos6-linux-gnu-cc in your PATH.
      
      Note that this compiler was either specified at configure time or in
      one of several possible environment variables.
      --------------------------------------------------------------------------
      failure.
      removing: _configtest.c _configtest.o
      error: Cannot compile MPI programs. Check your configuration!!!

>which x86_64-conda_cos6-linux-gnu-cc
/i didn't have it anywhere/
>conda install x86_64-conda_cos6-linux-gnu-cc
ls ~/miniconda3/envs/BAO/bin #look for x86_64-conda_cos6-linux-gnu-cc - I have x86_64-conda-linux-gnu-cc
>export PATH=~/miniconda3/envs/BAO/bin:$PATH
>pip install mpi4py #nope, same error as above
>conda install -c conda-forge openmpi
>conda install -c conda-forge openmpi --force-reinstall
>pip install mpi4py #yay!!! 

It finally worked. As you can imagine, a lot of steps, it took a while to figure it out. But now polychord is working and all is fine. 

Edit (03.08.2024):

Assuming the system is already up and running with gcc, g++, mpi, mpich, openmpi, I just reinstalled the environment super quick with python 3.12

conda create --name BAOn  

conda activate BAOn

conda install pip

conda install ipykernel

python3 -m ipykernel install --user --name=BAOn

which pip #to confirm you're working within the environment 

pip install wheel  

pip install pillow 

pip install numpy==1.26 --force #to confirm it's not using the outside numpy   

conda install matplotlib

pip install openmpi  #note here on my computer conda install openmpi makes the calculation speed 3 times slower, so either do pip install openmpi or conda install mpich

which mpicc #to confirm the mpicc refers to the env  

pip install mpi4py --force #use force in case you have an old library
 

# see https://stackoverflow.com/questions/61003570/cannot-install-mpi4py-using-conda-and-specify-pre-installed-mpicc-path  

pip install git+https://github.com/PolyChord/PolyChordLite@master #this didn't work for me

#this below did work:

git clone https://github.com/PolyChord/PolyChordLite.git
cd PolyChordLite
make
pip install .

conda install jupyter
pip install emcee --force
pip install getdist
pip install anesthetic
 

Also, to useful commands (which I still haven't tried but I will in the future):

conda env export > BAOn.yml

conda env create -f BAOn.yml