Addressing a series of functions, the President invoked Mahatma Gandhi and cited his vision of India as an inclusive nation where every section of population lived in equality and enjoyed equal opportunity.
Referring to government's cleanliness campaign, Mukherjee said, "Swachh Bharat, according to Bapu, implied a clean mind, clean body and clean environment."
"The real dirt of India lies not in our streets but in our minds and in our unwillingness to let go of views that divide society into 'them' and 'us', 'pure' and 'impure'," he said while inaugurating the Archives and Research Centre at Sabarmati Ashram.
Mukherjee, who also addressed the 62nd convocation of Gujarat Vidyapith here, said, "Gandhiji in life and in death struggled for communal harmony. Educating in peace and harmony is the key to contain and reorient the disruptive forces in society."
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Amid the debate on alleged intolerance, Mukherjee has repeatedly emphasised on the liberal traditions of India.
"Every day, we see unprecedented violence all around us.
At the heart of this violence is darkness, fear and mistrust. While we invent new modes of combating this ever spiralling violence, we must not forget the power of non-violence, dialogue and reason," Mukherjee said.
Referring to the motto of Gujarat Vidyapith 'Sa Vidya Ya Vimuktaye' (education that liberates), he said the institute should continue to demonstrate that it is by educating the heart and mind of the youth that social rejuvenation on the path of non-violence is possible.
"Every citizen has a duty to rededicate themselves to create a clean external and internal environment of self and society to make Swachh Bharat possible," he said.
"So long as the dehumanising practice of carrying night soil persists, we cannot have real Swacch Bharat," he said.
Speaking about education scenario of the country Mukherjee said it should include "character building".
"Gandhiji had said and I quote: "Literary education is of no value, if it is not able to build up a sound character," Mukherjee said.
He also cited numerous challenges faced by country's higher education sector and noted that there is need for increasing access and making education affordable besides ensuring quality and pursue excellence.
"These are not contradictory objectives but complementary goals. Quality consciousness must be at the back of every initiative in our higher academic institutions.
"Many meritorious students leave the shores of our country and study abroad due to lack of institutes in India conforming to high standards of education. Not many international students come to India for higher studies either," Mukherjee said.
"We must do all at our end to reverse this trend and make India emerge as a quality and affordable education destination for students outside," the President said and referred to ancient universities like Takshila and Nalanda while calling for renewed efforts to gain India's leadership role in higher education sector.
The developmental challenges faced by our country call for an inspired response from the higher education system.
Quality and relevant research can help tide over our socio-economic problems, he said.
"India is home to a large population of the young. Demographic dividend can occur only if greater number of competent and skilled professionals is produced by our higher educational and technical institutions.
"This calls for skill development initiatives on a massive scale," the President said.
Gandhiji used a very special word for civilisation, 'Sudhar' (improvement), the President said.
"Sudharis not just the good path or the right path but also that which holds human civilisation together. Let us pledge to join hands and build an India that truly exemplifies this Sudhar," he added.
Mukherjee also visited 'Hriday Kunj', a place inside the Ashram where Gandhiji lived during freedom struggle.
In the visitor's diary of Hriday Kunj, he wrote, "Each visit to this hallowed place gives me a renewed hope and determination to realise Gandhiji's dreams of an Indian free from want and oppression.